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, $\tau\to \mu\gamma$ and $Z\to \tau\mu$, 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.

Observation of the east-west anisotropy of the atmospheric neutrino flux

The east-west anisotropy, caused by the deflection of primary cosmic rays in the Earth's magnetic field, is observed for the first time in the flux of atmospheric neutrinos. Using a 45 kt-year exposure of the Super-Kamiokande detector, 552 e-like and 633 mu-like horizontally-going events are selected in the momentum range between 400 and 3000 MeV/c. The azimuthal distribution of e-like and mu-like events agrees with the expectation from atmospheric neutrino flux calculations that account for the geomagnetic field, verifying that the geomagnetic field effects in the production of atmospheric neutrinos in the GeV energy range are well understood.Comment: 8 pages,3 figures revtex, submitted to PR