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• Genomic and transcriptomic data on a cohort of dermatofibrosarcoma protuberans tumors. • Evaluation of genetic features in relation to various clinical features. • Data supporting an origin of the COL1A1-PDGFB fusion in the G2-S phase of the cell cycle. • Identification of potential target genes in amplified regions on chromosomes 17 and 22. The dermatofibrosarcoma protuberans family of tumors (DPFT) comprises cutaneous soft tissue neoplasms associated with aberrant PDGFBR signaling, typically through a COL1A1-PDGFB fusion. The aim of the present study was to obtain a better understanding of the chromosomal origin of this fusion and to assess the spectrum of secondary mutations at the chromosome and nucleotide levels. We thus investigated 42 tumor samples from 35 patients using chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, and/or massively parallel sequencing (gene panel, whole exome and transcriptome sequencing) methods. We confirmed the age-associated differences in the origin of the COL1A1 - PDGFB fusion and could show that it in most cases must arise after DNA synthesis, i.e., in the S or G2 phase of the cell cycle. Whereas there was a non-random pattern of secondary chromosomal rearrangements, single nucleotide variants seem to have little impact on tumor progression. No clear genomic differences between low-grade and high-grade DPFT were found, but the number of chromosomes and chromosomal imbalances as well as the frequency of 9p deletions all tended to be greater among the latter. Gene expression profiling of tumors with COL1A1 - PDGFB fusions associated with unbalanced translocations or ring chromosomes identified several transcriptionally up-regulated genes in the amplified regions of chromosomes 17 and 22, including TBX2, PRKCA, MSI2, SOX9, SOX10 , and PRAME. [ABSTRACT FROM AUTHOR]

Long-lasting synaptic plasticity is often accompanied by morphological changes as well as formation and/or loss of dendritic spines. Since the spine cytoskeleton mainly consists of actin filaments, morphological changes are primarily controlled by actin binding proteins (ABPs). Inositol-1,4,5-trisphosphate-3-kinase-A (ITPKA) is a neuron-specific, actin bundling protein concentrated at dendritic spines. Here, we demonstrate that ITPKA depletion in mice increases the number of hippocampal spine-synapses while reducing average spine length. By employing actin to ABP ratios similar to those occurring at post synaptic densities, in addition to cross-linking actin filaments, ITPKA strongly inhibits Arp2/3-complex induced actin filament branching by displacing the complex from F-actin. In summary, our data show that in vivo ITPKA negatively regulates formation and/or maintenance of synaptic contacts in the mammalian brain. On the molecular level this effect appears to result from the ITPKA-mediated inhibition of Arp2/3-complex F-actin branching activity. [ABSTRACT FROM AUTHOR]

Assessing effects of organic fertilizer applications on N2O emissions is of great interest because they can cause higher N2O emissions compared to inorganic fertilizers for a given amount of added nitrogen (N). But there are also reports about enhanced N2O reduction to climate-neutral elemental N2 after application of organic manures to soils. Factors controlling the N2O/(N2O + N2) product ratio of denitrification are interrelated, and also the ratio is difficult to study because of limitations in N2 flux measurements. In this study, we investigated N2O and N2 emissions from soil treated with organic fertilizers with different C/N ratios. An N2O isotopomer approach combined with conventional N2O and N2 flux measurements was employed to study underlying microbial pathways. A grassland soil was amended with anaerobic digestate (AD) from food waste digestion (low C/N ratio) or cattle slurry (CS; high C/N ratio), respectively, adjusted to 90% WFPS, and incubated for 52 days under helium-oxygen atmosphere (10% O2) using a soil incubation system capable of automated N2O, N2, and CO2 measurements. N2O isotopomer signatures, i.e. the d18O and SP values (site preference between 15N at the central and the peripheral position in the N2O molecule), were determined by Isotope Ratio Mass Spectrometry and used to model and subsequently estimate the contribution of bacterial denitrification and autotrophic nitrification to N2O production. For this approach the direct determination of emitted N2 is essential to take isotope effects during N2O reduction to N2 into account by correcting the measured isotope signatures for isotope effects during N2O reduction using previously determined fractionation factor ranges. The addition of both organic fertilizers to soil drastically increased the rate of gaseous N emissions (N2O + N2), probably due to the effects of concurrent presence of nitrate and labile C on the denitrification rate. In the initial phase of the experiment (day 1 to ~15), gaseous N emissions were dominated by N2 fluxes in soils amended with organic manures; meanwhile, N2O emissions were lower compared to untreated Control soils, but increased after 15-20 days relative to the initial fluxes, especially with CS. Extremely low N2O, but high N2 emissions in the initial phase suggest that reduction of N2O to N2 via denitrification was triggered when the soil was amended with organic fertilizers. In contrast in the untreated Control, N2O release was highest during the initial phase. Total N2O release from AD treated soil was similar to Control, while N2O from CS treated soil was considerably higher, indicating that denitrification was triggered more by the high labile carbon content in CS, while the cumulative N2O/(N2O + N2) product ratio and thus N2O reduction were similar with both organic fertilizers. The results of the N2O source partitioning based on the isotopomer data suggest that about 8-25% (AD) and 33-43% (CS) of the cumulated N2O emission was due to nitrification in organically amended soil, while in the untreated Control nitrification accounted for about 5-16%. The remaining N2O production was attributed mainly to denitrification, while the poor model fit for other source pathways like fungal denitrification suggested their contribution to be of minor importance. The observed rather distinct phases with predominance first of denitrification and later of nitrification may help developing mitigation measures by addressing N2O source processes individually with appropriate management options. The observation of relatively large shares of nitrification-derived N2O is surprising, but may possibly be related to the low soil pH and will require further investigation. The determination of N2 production is essential for this isotopomer-based source partitioning approach, but so far only applicable under laboratory conditions. The results of this study indicate that the combination of N2O d18O and SP values is very useful in obtaining more robust source estimates as compared to using SP values alone. [ABSTRACT FROM AUTHOR]

Abstract: Anaerobic digestates (AD) from biogas production are applied to agricultural land as organic fertilizers, but pose an ammonia (NH3) emission source. However, data about NH3 emissions of cold season AD land spreading is still lacking. Therefore, in the present study NH3 emissions of AD application under winter conditions were determined. AD was applied via trail hoses to a field plot of 27 ha in Northern Germany during the winter with temperatures around the freezing point and partly frozen soil. NH4 + N application rate was, including a preceding urea application, 123 kg NH4 + and urea N ha−1. The NH3 volatilization was monitored using Open Path Fourier Transform Infrared spectroscopy in combination with a micrometeorological transport model. Cumulative NH3 volatilization during the six day measurements was 17.5 kg NH3 N ha−1 which corresponds to 33.1% of the NH4 + N in applied AD. This NH3 loss is relatively high for low temperature conditions and was most likely caused by the frozen soil restricting AD infiltration. [Copyright &y& Elsevier]

Abstract: Nitrous oxide (N2O) is one of the major greenhouse gases emitted from soils, where it is mainly produced by nitrification and denitrification. It is well known that rates of N2O release from soils are mainly determined by the availability of substrates and oxygen, but N2O source apportioning, highly needed to advance N2O mitigation strategies, still remains challenging. In this study, using an automated soil incubation system, the N2O site preference, i.e. the intramolecular 15N distribution, was analyzed to evaluate the progression in N2O source processes following organic soil amendment. Biogas fermentation residue (BGR; originating from food waste fermentation) was applied to repacked grassland soil cores and compared to ammonium sulfate (AS) application, both at rates equivalent to 160kgNH4 +–Nha−1, and to unamended soil (control). The soil cores were incubated in a helium–oxygen atmosphere with 20kPa O2 for 43 days at 80% water-filled pore space. 43-day cumulative N2O emissions were highest with BGR treated soil accounting for about 1.68kgN2O–Nha−1 while application of AS caused much lower fluxes of c. 0.23kgN2O–Nha−1. Also, after BGR application, carbon dioxide (CO2) fluxes showed a pronounced initial peak with steep decline until day 21 whereas with ammonium addition they remained at the background level. N2O dual isotope and isotopomer analysis of gas samples collected from BGR treated soil indicated bacterial denitrification to be the main N2O generating process during the first three weeks when high CO2 fluxes signified high carbon availability. In contrast, in the second half after all added labile carbon substrates had been consumed, nitrification, i.e. the generation of N2O via oxidation of hydroxylamine, gained in importance reaching roughly the same N2O production rate compared to bacterial denitrification as indicated by N2O SP. Overall in this study, bacterial denitrification seemed to be the main N2O forming process after application of biogas residues and fluxes were mainly driven by available organic carbon. [Copyright &y& Elsevier]

The article discusses a critique of paper "Estimate of bacterial and fungal N2O production processes after crop residue input and fertilizer application to an agricultural field by 15 N isotopomer analysis".

Abstract: Quantifying denitrification in arable soils is crucial in predicting nitrogen fertiliser losses and N2O emissions. Stable isotopologue analyses of emitted N2O (δ15N, δ18O and SP= 15N site preference within the linear N2O molecule) may help to distinguish production pathways and to quantify N2O reduction to N2. However, such interpretations are often ambiguous due to insufficient knowledge on isotopic fractionation mechanisms. Here we present a complex experimental approach to determine the net fractionation factors (η) associated with denitrification. This determination is based on three laboratory experiments differing in their experimental set-up and soil properties. Static and dynamic incubation techniques were compared. All available methods for independent determination of N2O reduction contribution were used, namely, N2-free atmosphere incubation, acetylene inhibition technique and 15N gas-flux method. For N2O production: (i) the determined difference in δ18O between soil water and produced N2O vary from +18‰ to +42‰ and show very strict negative correlation with soil water saturation; (ii) the determined η15N of N2O production vary from −55‰ to −38‰ and the fractionation decreases with decreasing substrate availability; (iii) the determined SP of produced N2O vary from −3‰ to +9‰. For N2O reduction: (i) the determined η18O and η15N of N2O reduction vary in very wide ranges from −18‰ to +4‰ and from −11‰ to +12‰, respectively, and depend largely on the differences in experimental setups; whereas (ii) the determined ηSP of N2O reduction shows a very consistent value with all previous studies and varies in a rather narrow range from −2‰ to −8‰. It can be concluded that η values of N2O production determined during laboratory incubations yield only roughly estimates for respective values expectable under field study conditions. η18O and η15N associated with N2O reduction may vary largely, probably depending on spatial and temporal coincidence of N2O production and reduction, and are hence not yet predictable for natural conditions. However, the ηSP of N2O reduction appeared to be relatively robust and a most probable value of about −5‰ can be used to constrain N2O reduction based on SP of soil emitted N2O. [Copyright &y& Elsevier]