Nutrient (C, N and P) enrichment induces significant changes in the soil metabolite profile and microbial carbon partitioning

The cycling of soil organic matter (SOM) and carbon (C) within the soil is governed by the presence of key macronutrients, particularly nitrogen (N) and phosphorus (P). The relative ratio of these nutrients has a direct effect on the potential rates of microbial growth and nutrient processing in soil and thus is fundamental to ecosystem functioning. However, the effect of changing soil nutrient stoichiometry on the small organic molecule (i.e., metabolite) composition and cycling by the microbial community remains poorly understood. Here, we aimed to disentangle the effect of stoichiometrically balanced nutrient addition on the soil metabolomic profile and apparent microbial carbon use efficiency (CUE) by adding a labile C source (glucose) in combination with N and/or P. After incorporation of the added glucose into the microbial biomass (48 h), metabolite profiling was undertaken by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). 494 metabolites were identified across all treatments mainly consisting of lipids (n = 199), amino acids (n = 118) and carbohydrates (n = 43), >97% of which showed significant changes in concentration between at least one treatment. Overall, glucose-C addition generally increased the synthesis of other carbohydrates in soil, while addition of C and N together increased peptide synthesis, indicative of protein formation and turnover. The combination of C and P significantly increased the number of fatty acids synthesised. There was no significant change in the PLFA-derived microbial community structure or microbial biomass following C, N and P addition. Further, N addition led to an increase in glucose-C partitioning into anabolic processes (i.e., increased CUE), suggesting the microbial community was N, but not P limited. Based on the metabolomic profiles observed here, we conclude that inorganic nutrient enrichment causes substantial shifts in both primary and secondary metabolism within the microbial community, leading to changes in resource flow and thus soil functioning, however, the microbial community illustrated significant metabolic flexibility

Pairing symmetry and long range pair potential in a weak coupling theory of superconductivity

We study the superconducting phase with two component order parameter scenario, such as, $d_{x^2-y^2} + e^{i\theta}s_{\alpha}$, where $\alpha = xy, x^2+y^2$. We show, that in absence of orthorhombocity, the usual $d_{x^2-y^2}$ does not mix with usual $s_{x^2+y^2}$ symmetry gap in an anisotropic band structure. But the $s_{xy}$ symmetry does mix with the usual d-wave for $\theta =0$. The d-wave symmetry with higher harmonics present in it also mixes with higher order extended $s$ wave symmetry. The required pair potential to obtain higher anisotropic $d_{x^2-y^2}$ and extended s-wave symmetries, is derived by considering longer ranged two-body attractive potential in the spirit of tight binding lattice. We demonstrate that the dominant pairing symmetry changes drastically from $d$ to $s$ like as the attractive pair potential is obtained from longer ranged interaction. More specifically, a typical length scale of interaction $\xi$, which could be even/odd multiples of lattice spacing leads to predominant $s/d$ wave symmetry. The role of long range interaction on pairing symmetry has further been emphasized by studying the typical interplay in the temperature dependencies of these higher order $d$ and $s$ wave pairing symmetries.Comment: Revtex 8 pages, 7 figures embeded in the text, To appear in PR

Solar parameters for modeling interplanetary background

The goal of the Fully Online Datacenter of Ultraviolet Emissions (FONDUE) Working Team of the International Space Science Institute in Bern, Switzerland, was to establish a common calibration of various UV and EUV heliospheric observations, both spectroscopic and photometric. Realization of this goal required an up-to-date model of spatial distribution of neutral interstellar hydrogen in the heliosphere, and to that end, a credible model of the radiation pressure and ionization processes was needed. This chapter describes the solar factors shaping the distribution of neutral interstellar H in the heliosphere. Presented are the solar Lyman-alpha flux and the solar Lyman-alpha resonant radiation pressure force acting on neutral H atoms in the heliosphere, solar EUV radiation and the photoionization of heliospheric hydrogen, and their evolution in time and the still hypothetical variation with heliolatitude. Further, solar wind and its evolution with solar activity is presented in the context of the charge exchange ionization of heliospheric hydrogen, and in the context of dynamic pressure variations. Also the electron ionization and its variation with time, heliolatitude, and solar distance is presented. After a review of all of those topics, we present an interim model of solar wind and the other solar factors based on up-to-date in situ and remote sensing observations of solar wind. Results of this effort will further be utilised to improve on the model of solar wind evolution, which will be an invaluable asset in all heliospheric measurements, including, among others, the observations of Energetic Neutral Atoms by the Interstellar Boundary Explorer (IBEX).Comment: Chapter 2 in the planned "Cross-Calibration of Past and Present Far UV Spectra of Solar System Objects and the Heliosphere", ISSI Scientific Report No 12, ed. R.M. Bonnet, E. Quemerais, M. Snow, Springe

An Observational Overview of Solar Flares

We present an overview of solar flares and associated phenomena, drawing upon a wide range of observational data primarily from the RHESSI era. Following an introductory discussion and overview of the status of observational capabilities, the article is split into topical sections which deal with different areas of flare phenomena (footpoints and ribbons, coronal sources, relationship to coronal mass ejections) and their interconnections. We also discuss flare soft X-ray spectroscopy and the energetics of the process. The emphasis is to describe the observations from multiple points of view, while bearing in mind the models that link them to each other and to theory. The present theoretical and observational understanding of solar flares is far from complete, so we conclude with a brief discussion of models, and a list of missing but important observations.Comment: This is an article for a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing

The Immune Landscape of Cancer

We performed an extensive immunogenomic anal-ysis of more than 10,000 tumors comprising 33diverse cancer types by utilizing data compiled byTCGA. Across cancer types, we identified six im-mune subtypes\u2014wound healing, IFN-gdominant,inflammatory, lymphocyte depleted, immunologi-cally quiet, and TGF-bdominant\u2014characterized bydifferences in macrophage or lymphocyte signa-tures, Th1:Th2 cell ratio, extent of intratumoral het-erogeneity, aneuploidy, extent of neoantigen load,overall cell proliferation, expression of immunomod-ulatory genes, and prognosis. Specific drivermutations correlated with lower (CTNNB1,NRAS,orIDH1) or higher (BRAF,TP53,orCASP8) leukocytelevels across all cancers. Multiple control modalitiesof the intracellular and extracellular networks (tran-scription, microRNAs, copy number, and epigeneticprocesses) were involved in tumor-immune cell inter-actions, both across and within immune subtypes.Our immunogenomics pipeline to characterize theseheterogeneous tumors and the resulting data areintended to serve as a resource for future targetedstudies to further advance the field

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFb signaling, p53 and beta-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy