283 research outputs found
Genome characterization of two novel deep-sea sediment fungi, Penicillium pacificagyrus sp. nov. and Penicillium pacificasedimenti sp. nov., from South Pacific Gyre subseafloor sediments, highlights survivability
Background
Marine deep subsurface sediments were once thought to be devoid of eukaryotic life, but advances in molecular technology have unlocked the presence and activity of well-known closely related terrestrial and marine fungi. Commonly detected fungi in deep marine sediment environments includes Penicillium, Aspergillus, Cladosporium, Fusarium, and Schizophyllum, which could have important implications in carbon and nitrogen cycling in this isolated environment. In order to determine the diversity and unknown metabolic capabilities of fungi in deep-sea sediments, their genomes need to be fully analyzed. In this study, two Penicillium species were isolated from South Pacific Gyre sediment enrichments during Integrated Ocean Drilling Program Expedition 329. The inner gyre has very limited productivity, organic carbon, and nutrients.
Results
Here, we present high-quality genomes of two proposed novel Penicillium species using Illumina HiSeq and PacBio sequencing technologies. Single-copy homologues within the genomes were compared to other closely related genomes using OrthoMCL and maximum-likelihood estimation, which showed that these genomes were novel species within the genus Penicillium. We propose to name isolate SPG-F1 as Penicillium pacificasedimenti sp. nov. and SPG-F15 as Penicillium pacificagyrus sp. nov. The resulting genome sizes were 32.6 Mbp and 36.4 Mbp, respectively, and both genomes were greater than 98% complete as determined by the presence of complete single-copy orthologs. The transposable elements for each genome were 4.87% for P. pacificasedimenti and 10.68% for P. pacificagyrus. A total of 12,271 genes were predicted in the P. pacificasedimenti genome and 12,568 genes in P. pacificagyrus. Both isolates contained genes known to be involved in the degradation of recalcitrant carbon, amino acids, and lignin-derived carbon.
Conclusions
Our results provide the first constructed genomes of novel Penicillium isolates from deep marine sediments, which will be useful for future studies of marine subsurface fungal diversity and function. Furthermore, these genomes shed light on the potential impact fungi in marine sediments and the subseafloor could have on global carbon and nitrogen biogeochemical cycles and how they may be persisting in the most energy-limited sedimentary biosphere
Comparison of 3-Dimensional and 1-Dimensional Schemes in the calculation of Atmospheric Neutrinos
A 3-dimensional calculation of atmospheric neutrinos flux is presented, and
the results are compared with those of a 1-dimensional one. In this study,
interaction and propagation of particles is treated in a 3-dimensional way
including the curvature of charged particles due to the geomagnetic field,
which is assumed to be a dipole field. The purpose of this paper is limited to
the comparison of calculation schemes. The updated flux value with new
interaction model and primary flux model will be reported in a separate paper.
Except for nearly horizontal directions, the flux is very similar to the
result of 1 dimensional calculations. However, for near-horizontal directions
an enhancement of the neutrino flux is seen even at energies as high as 1 GeV.
The production height of neutrinos is lower than the prediction by
1-dimensional calculation for near-horizontal directions, and is a little
higher for near-vertical directions. However, the difference is not evident
except for near-horizontal directions.Comment: 22 pages, 15figure
Deviation of Neutrino Mixing from Bi-maximal
We have studied how observables of the neutrino mixing matrix can link up
with the ones in the quark sector. The deviation from the bi-maximal flavor
mixing is parameterized using a 3 x 3 unitary matrix. The neutrino mixings are
investigated supposing this unitary matrix to be hierarchical like the quark
mixing matrix. We obtain the remarkable prediction |U_{e3}| >= 0.03 from the
experimentally allowed range tan^2 theta_{sol} = 0.24 ~ 0.89. The CP violation
in neutrino oscillations is expected to be very small.Comment: Some references are adde
Lepton Flavor Violation in Supersymmetric SO(10) Grand Unified Models
The study for lepton flavor violation combined with the neutrino oscillation
may provide more information about the lepton flavor structure of the grand
unified theory. In this paper, we study two lepton flavor violation processes,
and , in the context of supersymmetric SO(10)
grand unified models. We find the two processes are both of phenomenological
interest. In particular the latter may be important in some supersymmetric
parameter space where the former is suppressed. Thus, Z-dacay may offer another
chance for looking for lepton flavor violation.Comment: 26 pages, 10 figure
Simulation of Atmospheric Muon and Neutrino Fluxes with CORSIKA
The fluxes of atmospheric muons and neutrinos are calculated by a three
dimensional Monte Carlo simulation with the air shower code CORSIKA using the
hadronic interaction models DPMJET, VENUS, GHEISHA, and UrQMD. For the
simulation of low energy primary particles the original CORSIKA has been
extended by a parametrization of the solar modulation and a microscopic
calculation of the directional dependence of the geomagnetic cut-off functions.
An accurate description for the geography of the Earth has been included by a
digital elevation model, tables for the local magnetic field in the atmosphere,
and various atmospheric models for different geographic latitudes and annual
seasons. CORSIKA is used to calculate atmospheric muon fluxes for different
locations and the neutrino fluxes for Kamioka. The results of CORSIKA for the
muon fluxes are verified by an extensive comparison with recent measurements.
The obtained neutrino fluxes are compared with other calculations and the
influence of the hadronic interaction model, the geomagnetic cut-off and the
local magnetic field on the neutrino fluxes is investigated.Comment: revtex, 19 pages, 19 Postscript figures, submitted to Phys. Rev.
Atmospheric neutrino flux from 3-dimensional simulation
The atmospheric muon and neutrino flux have been simulated using the same
approach which successfully accounted for the recent secondary proton, electron
and positron flux measurements in orbit by the AMS experiment. For the muon
flux, a good agreement is obtained with the CAPRICE and HEAT data for altitudes
ranging from sea level up to about 38 km. The general features of the
calculated atmospheric neutrino flux are reported and discussed. The flux
obtained at the Super-Kamiokande experiment location are reported and compared
with other calculations. For low neutrino energies the flux obtained is
significantly smaller than that used in the data analysis of underground
experiment. The simulation results for the SOUDAN experiment site are also
reported.Comment: 33 pages, 27 figures, 12 tables, final version for Phys. Rev.
Evidence for oscillation of atmospheric neutrinos
We present an analysis of atmospheric neutrino data from a 33.0 kiloton-year
(535-day) exposure of the Super-Kamiokande detector. The data exhibit a zenith
angle dependent deficit of muon neutrinos which is inconsistent with
expectations based on calculations of the atmospheric neutrino flux.
Experimental biases and uncertainties in the prediction of neutrino fluxes and
cross sections are unable to explain our observation. The data are consistent,
however, with two-flavor nu_mu nu_tau oscillations with sin^2(2theta)>0.82
and 5x10^-4 < delta m^2 < 6x10^-3 eV^2 at 90% confidence level.Comment: 9 pages (two-column) with 4 figures. Small corrections to Eqn.4 and
Fig.3. Final version to appear in PR
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