Nutrient limitation reduces land carbon uptake in simulations with a model of combined carbon, nitrogen and phosphorus cycling

Terrestrial carbon (C) cycle models applied for climate projections simulate a strong increase in net primary productivity (NPP) due to elevated atmospheric CO<sub>2</sub> concentration during the 21st century. These models usually neglect the limited availability of nitrogen (N) and phosphorus (P), nutrients that commonly limit plant growth and soil carbon turnover. To investigate how the projected C sequestration is altered when stoichiometric constraints on C cycling are considered, we incorporated a P cycle into the land surface model JSBACH (Jena Scheme for Biosphere–Atmosphere Coupling in Hamburg), which already includes representations of coupled C and N cycles. <br><br> The model reveals a distinct geographic pattern of P and N limitation. Under the SRES (Special Report on Emissions Scenarios) A1B scenario, the accumulated land C uptake between 1860 and 2100 is 13% (particularly at high latitudes) and 16% (particularly at low latitudes) lower in simulations with N and P cycling, respectively, than in simulations without nutrient cycles. The combined effect of both nutrients reduces land C uptake by 25% compared to simulations without N or P cycling. Nutrient limitation in general may be biased by the model simplicity, but the ranking of limitations is robust against the parameterization and the inflexibility of stoichiometry. After 2100, increased temperature and high CO<sub>2</sub> concentration cause a shift from N to P limitation at high latitudes, while nutrient limitation in the tropics declines. The increase in P limitation at high-latitudes is induced by a strong increase in NPP and the low P sorption capacity of soils, while a decline in tropical NPP due to high autotrophic respiration rates alleviates N and P limitations. The quantification of P limitation remains challenging. The poorly constrained processes of soil P sorption and biochemical mineralization are identified as the main uncertainties in the strength of P limitation. Even so, our findings indicate that global land C uptake in the 21st century is likely overestimated in models that neglect P and N limitations. In the long term, insufficient P availability might become an important constraint on C cycling at high latitudes. Accordingly, we argue that the P cycle must be included in global models used for C cycle projections

Nesting properties and anisotropy of the Fermi surface of LuNi2_{2}B2_{2}C

The rare earth nickel borocarbides, with the generic formula $R$Ni$_{2}$B$_{2}$C, have recently been shown to display a rich variety of phenomena. Most striking has been the competition between, and even coexistence of, antiferromagnetism and superconductivity. We have measured the Fermi surface (FS) of LuNi$_{2}$B$_{2}$C, and shown that it possesses nesting features capable of explaining some of the phenomena experimentally observed. In particular, it had previously been conjectured that a particular sheet of FS is responsible for the modulated magnetic structures manifest in some of the series. We report the first direct experimental observation of this sheet.Comment: 4 pages, 4 PS figure

Theory of de Haas-van Alphen Effect in Type-II Superconductors

Theory of quasiparticle spectra and the de Haas-van Alphen (dHvA) oscillation in type-II superconductors are developed based on the Bogoliubov-de Gennes equations for vortex-lattice states. As the pair potential grows through the superconducting transition, each degenerate Landau level in the normal state splits into quasiparticle bands in the magnetic Brillouin zone. This brings Landau-level broadening, which in turn leads to the extra dHvA oscillation damping in the vortex state. We perform extensive numerical calculations for three-dimensional systems with various gap structures. It is thereby shown that (i) this Landau-level broadening is directly connected with the average gap at H=0 along each Fermi-surface orbit perpendicular to the field H; (ii) the extra dHvA oscillation attenuation is caused by the broadening around each extremal orbit. These results imply that the dHvA experiment can be a unique probe to detect band- and/or angle-dependent gap amplitudes. We derive an analytic expression for the extra damping based on the second-order perturbation with respect to the pair potential for the Luttinger-Ward thermodynamic potential. This formula reproduces all our numerical results excellently, and is used to estimate band-specific gap amplitudes from available data on NbSe_2, Nb_3Sn, and YNi_2B_2C. The obtained value for YNi_2B_2C is fairly different from the one through a specific-heat measurement, indicating presence of gap anisotropy in this material. C programs to solve the two-dimensional Bogoliubov-de Gennes equations are available at http://phys.sci.hokudai.ac.jp/~kita/index-e.html .Comment: 16 pages, 11 figure

Motor signatures of emotional reactivity in frontotemporal dementia

Automatic motor mimicry is essential to the normal processing of perceived emotion, and disrupted automatic imitation might underpin socio-emotional deficits in neurodegenerative diseases, particularly the frontotemporal dementias. However, the pathophysiology of emotional reactivity in these diseases has not been elucidated. We studied facial electromyographic responses during emotion identification on viewing videos of dynamic facial expressions in 37 patients representing canonical frontotemporal dementia syndromes versus 21 healthy older individuals. Neuroanatomical associations of emotional expression identification accuracy and facial muscle reactivity were assessed using voxel-based morphometry. Controls showed characteristic profiles of automatic imitation, and this response predicted correct emotion identification. Automatic imitation was reduced in the behavioural and right temporal variant groups, while the normal coupling between imitation and correct identification was lost in the right temporal and semantic variant groups. Grey matter correlates of emotion identification and imitation were delineated within a distributed network including primary visual and motor, prefrontal, insular, anterior temporal and temporo-occipital junctional areas, with common involvement of supplementary motor cortex across syndromes. Impaired emotional mimesis may be a core mechanism of disordered emotional signal understanding and reactivity in frontotemporal dementia, with implications for the development of novel physiological biomarkers of socio-emotional dysfunction in these diseases

A Cytosine Methyltransferase Homologue Is Essential for Sexual Development in Aspergillus nidulans

Background: The genome defense processes RIP (repeat-induced point mutation) in the filamentous fungus Neurospora crassa, and MIP (methylation induced premeiotically) in the fungus Ascobolus immersus depend on proteins with DNA methyltransferase (DMT) domains. Nevertheless, these proteins, RID and Masc1, respectively, have not been demonstrated to have DMT activity. We discovered a close homologue in Aspergillus nidulans, a fungus thought to have no methylation and no genome defense system comparable to RIP or MIP. Principal Findings: We report the cloning and characterization of the DNA methyltransferase homologue A (dmtA) gene from Aspergillus nidulans. We found that the dmtA locus encodes both a sense (dmtA) and an anti-sense transcript (tmdA). Both transcripts are expressed in vegetative, conidial and sexual tissues. We determined that dmtA, but not tmdA, is required for early sexual development and formation of viable ascospores. We also tested if DNA methylation accumulated in any of the dmtA/tmdA mutants we constructed, and found that in both asexual and sexual tissues, these mutants, just like wild-type strains, appear devoid of DNA methylation. Conclusions/Significance: Our results demonstrate that a DMT homologue closely related to proteins implicated in RIP and MIP has an essential developmental function in a fungus that appears to lack both DNA methylation and RIP or MIP. It remains formally possible that DmtA is a bona fide DMT, responsible for trace, undetected DNA methylation that i

Antiproliferative Effects of DNA Methyltransferase 3B Depletion Are Not Associated with DNA Demethylation

Silencing of genes by hypermethylation contributes to cancer progression and has been shown to occur with increased frequency at specific genomic loci. However, the precise mechanisms underlying the establishment and maintenance of aberrant methylation marks are still elusive. The de novo DNA methyltransferase 3B (DNMT3B) has been suggested to play an important role in the generation of cancer-specific methylation patterns. Previous studies have shown that a reduction of DNMT3B protein levels induces antiproliferative effects in cancer cells that were attributed to the demethylation and reactivation of tumor suppressor genes. However, methylation changes have not been analyzed in detail yet. Using RNA interference we reduced DNMT3B protein levels in colon cancer cell lines. Our results confirm that depletion of DNMT3B specifically reduced the proliferation rate of DNMT3B-overexpressing colon cancer cell lines. However, genome-scale DNA methylation profiling failed to reveal methylation changes at putative DNMT3B target genes, even in the complete absence of DNMT3B. These results show that DNMT3B is dispensable for the maintenance of aberrant DNA methylation patterns in human colon cancer cells and they have important implications for the development of targeted DNA methyltransferase inhibitors as epigenetic cancer drugs

Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction.</p> <p>Results</p> <p>We introduce <monospace>Bio::Homology::InterologWalk</monospace>, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, <it>Drosophila melanogaster</it>. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation.</p> <p>Conclusions</p> <p>Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the putative PPI datasets to be easily integrated into existing analysis workflows. The <monospace>Bio::Homology::InterologWalk</monospace> module, sample scripts and full documentation are freely available from the Comprehensive Perl Archive Network (CPAN) under the GNU Public license.</p

The Glycosylation Pattern of Common Allergens: The Recognition and Uptake of Der p 1 by Epithelial and Dendritic Cells Is Carbohydrate Dependent

Allergens are initiators of both innate and adaptive immune responses. They are recognised at the site of entry by epithelial and dendritic cells (DCs), both of which activate innate inflammatory circuits that can collectively induce Th2 immune responses. In an attempt to have a better understanding of the role of carbohydrates in the recognition and uptake of allergens by the innate immune system, we defined common glycosylation patterns in major allergens. This was done using labelled lectins and showed that allergens like Der p 1 (Dermatophagoides pteronyssinus group 1), Fel d 1 (Felis domisticus), Ara h 1 (Arachis hypogaea), Der p 2 (Dermatophagoides pteronyssinus group 2), Bla g 2 (Blattella germanica) and Can f 1 (Canis familiaris) are glycosylated and that the main dominant sugars on these allergens are 1–2, 1–3 and 1–6 mannose. These observations are in line with recent reports implicating the mannose receptor (MR) in allergen recognition and uptake by DCs and suggesting a major link between glycosylation and allergen recognition. We then looked at TSLP (Thymic Stromal Lymphopoietin) cytokine secretion by lung epithelia upon encountering natural Der p 1 allergen. TSLP is suggested to drive DC maturation in support of allergic hypersensitivity reactions. Our data showed an increase in TSLP secretion by lung epithelia upon stimulation with natural Der p 1 which was carbohydrate dependent. The deglycosylated preparation of Der p 1 exhibited minimal uptake by DCs compared to the natural and hyperglycosylated recombinant counterparts, with the latter being taken up more readily than the other preparations. Collectively, our data indicate that carbohydrate moieties on allergens play a vital role in their recognition by innate immune cells, implicating them in downstream deleterious Th2 cell activation and IgE production

The Drosophila Cytosine-5 Methyltransferase Dnmt2 Is Associated with the Nuclear Matrix and Can Access DNA during Mitosis

Cytosine-5 methyltransferases of the Dnmt2 family are highly conserved in evolution and their biological function is being studied in several organisms. Although all structural DNA methyltransferase motifs are present in Dnmt2, these enzymes show a strong tRNA methyltransferase activity. In line with an enzymatic activity towards substrates other than DNA, Dnmt2 has been described to localize to the cytoplasm. Using molecular and biochemical approaches we show here that Dnmt2 is both a cytoplasmic and a nuclear protein. Sub-cellular fractionation shows that a significant amount of Dnmt2 is bound to the nuclear matrix. Sub-cellular localization analysis reveals that Dnmt2 proteins are enriched in actively dividing cells. Dnmt2 localization is highly dynamic during the cell cycle. Using live imaging we observed that Dnmt2-EGFP enters prophase nuclei and shows a spindle-like localization pattern during mitotic divisions. Additional experiments suggest that this localization is microtubule dependent and that Dnmt2 can access DNA during mitotic cell divisions. Our results represent the first comprehensive characterization of Dnmt2 proteins on the cellular level and have important implications for our understanding of the molecular activities of Dnmt2