Methane exchange in a poorly-drained black spruce forest over permafrost observed using the eddy covariance technique

Ecosystem-scale methane (CH4) exchange was observed in a poorly-drained black spruce forest over permafrost in interior Alaska during the snow-free seasons of 2011–2013, using the eddy covariance technique. The magnitude of average CH4 exchange differed depending on wind direction, reflecting spatial variation in soil moisture condition around the observation tower, due to elevation change within the small catchment. In the drier upper position, the seasonal variation in CH4 emission was explained by the variation in soil water content only. In the wetter bottom, however, in addition to soil temperature and soil water content, seasonal thaw depth of frozen soil was also an important variable explaining the seasonal variation in CH4 exchange for this ecosystem. Total snow-free season (day of year 134–280) CH4 exchanges were 12.0 ± 1.0, 19.6 ± 3.0, and 36.6 ± 4.4 mmol m−2 season−1 for the drier upper position, moderately wet area, and wetter bottom of the catchment, respectively. Observed total season CH4 emission was nearly one order smaller than those reported in other northern wetlands, due probably to the relatively low ground water level and low soil temperature. The interannual variation of total snow-free season CH4 emission in the wetter bottom of the catchment was influenced by the amount of rainfall and thaw depth. On the other hand, in the drier upper position the amount of rainfall did not strongly affect the total season CH4 emission. Different responses of CH4 exchange to environmental conditions, depending on the position of a small catchment, should be considered when estimating the spatial variation in CH4 exchange accurately in ecosystems over permafrost.ArticleAGRICULTURAL AND FOREST METEOROLOGY. 214(0):157-168 (2015)journal articl

Endogenization and excision of human herpesvirus 6 in human genomes

Sequences homologous to human herpesvirus 6 (HHV-6) are integrated within the nuclear genome of about 1% of humans, but it is not clear how this came about. It is also uncertain whether integrated HHV-6 can reactive into an infectious virus. HHV-6 integrates into telomeres, and this has recently been associated with polymorphisms affecting MOV10L1. MOV10L1 is located on the subtelomere of chromosome 22q (chr22q) and is required to make PIWI-interacting RNAs (piRNAs). As piRNAs block germline integration of transposons, piRNA-mediated repression of HHV-6 integration has been proposed to explain this association.In vitro, recombination of the HHV-6 genome along its terminal direct repeats (DRs) leads to excision from the telomere and viral reactivation, but the expected "solo-DR scar" has not been describedin vivo. Here we screened for integrated HHV-6 in 7,485 Japanese subjects using whole-genome sequencing (WGS). Integrated HHV-6 was associated with polymorphisms on chr22q. However, in contrast to prior work, we find that the reported MOV10L1 polymorphism is physically linked to an ancient endogenous HHV-6A variant integrated into the telomere of chr22q in East Asians. Unexpectedly, an HHV-6B variant has also endogenized in chr22q; two endogenous HHV-6 variants at this locus thus account for 72% of all integrated HHV-6 in Japan. We also report human genomes carrying only one portion of the HHV-6B genome, a solo-DR, supporting in vivo excision and possible viral reactivation. Together these results explain the recently-reported association between integrated HHV-6 and MOV10L1/piRNAs, suggest potential exaptation of HHV-6 in its coevolution with human chr22q, and clarify the evolution and risk of reactivation of the only intact (non-retro)viral genome known to be present in human germlines

A THREE-PHASE INDUCTIVE SENSOR FOR IN VIVO MEASUREMENT OF ELECTRICAL ANISOTROPY OF BIOLOGICAL TISSUES

Biological tissue will have anisotropy in electrical conductivity, due to the orientation of muscular fibers or neural axons as well as the distribution of large size blood vessels. Thus, the in vivo measurement of electrical conductivity anisotropy can be used to detect deep-seated vessels in large organs such as the liver during surgeries. For diagnostic applications, decrease of anisotropy may indicate the existence of cancer in anisotropic tissues such as the white matter of the brain or the mammary gland in the breast.In this paper, we will introduce a new tri-phase induction method to drive rotating high-frequency electrical current in the tissue for the measurement of electrical conductivity anisotropy. In the measurement, three electromagnets are symmetrically placed on the tissue surface and driven by high-frequency alternative currents of  0 kHz, modulated  with 1 kHz 3-phase signals. In the center area of three magnets, magnetic fields are superimposed to produce a rotating induction current. This current produces electrical potentials among circularly arranged electrodes to be used to find the conductivity in each direction determined by the electrode pairs. To find the horizontal and vertical signal components, the measured potentials are amplified by a 2ch lock-in amplifier phase-locked with the 1 kHz reference signal. The superimposed current in the tissue was typically 45 micro Amperes when we applied 150 micro Tesla of magnetic field. We showed the validity of our method by conducting in vitro measurements with respect to artificially formed anisotropic materials and preliminary in vivo measurements on the pig’s liver.Compared to diffusion tensor MRI method, our anisotropy sensor is compact and advantageous for use during surgical operations because our method does not require strong magnetic field that may disturb ongoing surgical operations.Biological tissue will have anisotropy in electrical conductivity, due to the orientation of muscular fibers or neural axons as well as the distribution of large size blood vessels. Thus, the in vivo measurement of electrical conductivity anisotropy can be used to detect deep-seated vessels in large organs such as the liver during surgeries. For diagnostic applications, decrease of anisotropy may indicate the existence of cancer in anisotropic tissues such as the white matter of the brain or the mammary gland in the breast.In this paper, we will introduce a new tri-phase induction method to drive rotating high-frequency electrical current in the tissue for the measurement of electrical conductivity anisotropy. In the measurement, three electromagnets are symmetrically placed on the tissue surface and driven by high-frequency alternative currents of  0 kHz, modulated  with 1 kHz 3-phase signals. In the center area of three magnets, magnetic fields are superimposed to produce a rotating induction current. This current produces electrical potentials among circularly arranged electrodes to be used to find the conductivity in each direction determined by the electrode pairs. To find the horizontal and vertical signal components, the measured potentials are amplified by a 2ch lock-in amplifier phase-locked with the 1 kHz reference signal. The superimposed current in the tissue was typically 45 micro Amperes when we applied 150 micro Tesla of magnetic field. We showed the validity of our method by conducting in vitro measurements with respect to artificially formed anisotropic materials and preliminary in vivo measurements on the pig’s liver.Compared to diffusion tensor MRI method, our anisotropy sensor is compact and advantageous for use during surgical operations because our method does not require strong magnetic field that may disturb ongoing surgical operations

The association of ectopic craniopharyngioma in the fourth ventricle with familial adenomatous polyposis: illustrative case

[BACKGROUND] Craniopharyngioma (CP) often arises in the sellar and suprasellar areas; ectopic CP in the posterior fossa is rare. Familial adenomatous polyposis (FAP) is a genetic disorder involving the formation of numerous adenomatous polyps in the gastrointestinal tract, and it is associated with other extraintestinal manifestations. [OBSERVATIONS] The authors reported the case of a 63-year-old woman with FAP who presented with headache and harbored a growing mass in the fourth ventricle. Magnetic resonance imaging (MRI) findings revealed a well-circumscribed mass with high intensity on T1-weighted images and low intensity on T2-weighted images and exhibited no contrast enhancement. Gross total resection was performed and histopathology revealed an adamantinomatous CP (aCP). The authors also reviewed the previous reports of ectopic CP in the posterior fossa and found a high percentage of FAP cases among the ectopic CP group, thus suggesting a possible association between the two diseases. [LESSONS] An ectopic CP may be reasonably included in the differential diagnosis in patients with FAP who present with well-circumscribed tumors in the posterior fossa

Large-Scale Gene Disruption in Magnaporthe oryzae Identifies MC69, a Secreted Protein Required for Infection by Monocot and Dicot Fungal Pathogens

To search for virulence effector genes of the rice blast fungus, Magnaporthe oryzae, we carried out a large-scale targeted disruption of genes for 78 putative secreted proteins that are expressed during the early stages of infection of M. oryzae. Disruption of the majority of genes did not affect growth, conidiation, or pathogenicity of M. oryzae. One exception was the gene MC69. The mc69 mutant showed a severe reduction in blast symptoms on rice and barley, indicating the importance of MC69 for pathogenicity of M. oryzae. The mc69 mutant did not exhibit changes in saprophytic growth and conidiation. Microscopic analysis of infection behavior in the mc69 mutant revealed that MC69 is dispensable for appressorium formation. However, mc69 mutant failed to develop invasive hyphae after appressorium formation in rice leaf sheath, indicating a critical role of MC69 in interaction with host plants. MC69 encodes a hypothetical 54 amino acids protein with a signal peptide. Live-cell imaging suggested that fluorescently labeled MC69 was not translocated into rice cytoplasm. Site-directed mutagenesis of two conserved cysteine residues (Cys36 and Cys46) in the mature MC69 impaired function of MC69 without affecting its secretion, suggesting the importance of the disulfide bond in MC69 pathogenicity function. Furthermore, deletion of the MC69 orthologous gene reduced pathogenicity of the cucumber anthracnose fungus Colletotrichum orbiculare on both cucumber and Nicotiana benthamiana leaves. We conclude that MC69 is a secreted pathogenicity protein commonly required for infection of two different plant pathogenic fungi, M. oryzae and C. orbiculare pathogenic on monocot and dicot plants, respectively

Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales

We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-IMRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-IMRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-IMRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe

Methane exchange in a poorly-drained black spruce forest over permafrost observed using the eddy covariance technique

Ecosystem-scale methane (CH4) exchange was observed in a poorly-drained black spruce forest over permafrost in interior Alaska during the snow-free seasons of 2011–2013, using the eddy covariance technique. The magnitude of average CH4 exchange differed depending on wind direction, reflecting spatial variation in soil moisture condition around the observation tower, due to elevation change within the small catchment. In the drier upper position, the seasonal variation in CH4 emission was explained by the variation in soil water content only. In the wetter bottom, however, in addition to soil temperature and soil water content, seasonal thaw depth of frozen soil was also an important variable explaining the seasonal variation in CH4 exchange for this ecosystem. Total snow-free season (day of year 134–280) CH4 exchanges were 12.0 ± 1.0, 19.6 ± 3.0, and 36.6 ± 4.4 mmol m−2 season−1 for the drier upper position, moderately wet area, and wetter bottom of the catchment, respectively. Observed total season CH4 emission was nearly one order smaller than those reported in other northern wetlands, due probably to the relatively low ground water level and low soil temperature. The interannual variation of total snow-free season CH4 emission in the wetter bottom of the catchment was influenced by the amount of rainfall and thaw depth. On the other hand, in the drier upper position the amount of rainfall did not strongly affect the total season CH4 emission. Different responses of CH4 exchange to environmental conditions, depending on the position of a small catchment, should be considered when estimating the spatial variation in CH4 exchange accurately in ecosystems over permafrost.ArticleAGRICULTURAL AND FOREST METEOROLOGY. 214(0):157-168 (2015)journal articl