Fertilization of SRC Willow,II: Leaching and Element Balances

Short rotation coppice (SRC) willow is an emerging cropping system in focus for production of biomass for energy. To increase production, the willow is commonly fertilized, but studies have shown differing effects of fertilization on biomass production, ranging from almost no response to considerable positive effects. Focus has also been on replacing mineral fertilizer with organic waste products, such as manure and sludge. However, the effect on biomass production and environmental impact of various dosage and types of fertilizer is not well described. Therefore we studied the environmental impacts of different doses of mineral fertilizer, manure and sewage sludge in a commercially grown SRC willow stand. We examined macro nutrient and heavy metal leaching rates and calculated element balances to evaluate the environmental impact. Growth responses were reported in a former paper (Sevel et al. “Fertilization of SRC Willow, I: Biomass Production Response” Bioenergy Research, 2013). Nitrogen leaching was generally low, between 1 and 7 kg N ha^?1 year^?1 when doses of up to 120 kg N ha^?1 year^?1 were applied. Higher doses of 240 and 360 kg N ha^?1 as single applications caused leaching of 66 and 99 kg N ha^?1 year^?1, respectively, indicating N saturation of the system. Previous intensive farming including high doses of fertilizer may be responsible for a high soil N status and the high N leaching rates. However, moderate fertilization input could not compensate P and K exports with the biomass harvest. No elevated leaching of heavy metals was observed for any fertilization treatments and more cadmium than applied with the fertilizer was removed with the biomass from the system.     

Surfactant protein d deficiency in mice is associated with hyperphagia, altered fat deposition, insulin resistance, and increased basal endotoxemia

Pulmonary surfactant protein D (SP-D) is a host defence lectin of the innate immune system that enhances clearance of pathogens and modulates inflammatory responses. Recently it has been found that systemic SP-D is associated with metabolic disturbances and that SP-D deficient mice are mildly obese. However, the mechanism behind SP-D's role in energy metabolism is not known.Here we report that SP-D deficient mice had significantly higher ad libitum energy intake compared to wild-type mice and unchanged energy expenditure. This resulted in accumulation but also redistribution of fat tissue. Blood pressure was unchanged. The change in energy intake was unrelated to the basal levels of hypothalamic Pro-opiomelanocortin (POMC) and Agouti-related peptide (AgRP) gene expression. Neither short time systemic, nor intracereberoventricular SP-D treatment altered the hypothalamic signalling or body weight accumulation.In ad libitum fed animals, serum leptin, insulin, and glucose were significantly increased in mice deficient in SP-D, and indicative of insulin resistance. However, restricted diets eliminated all metabolic differences except the distribution of body fat. SP-D deficiency was further associated with elevated levels of systemic bacterial lipopolysaccharide.In conclusion, our findings suggest that lack of SP-D mediates modulation of food intake not directly involving hypothalamic regulatory pathways. The resulting accumulation of adipose tissue was associated with insulin resistance. The data suggest SP-D as a regulator of energy intake and body composition and an inhibitor of metabolic endotoxemia. SP-D may play a causal role at the crossroads of inflammation, obesity, and insulin resistance.     

Modelling the carbon and nitrogen balances of direct land use changes from energy crops in Denmark: a consequential life cycle inventory

This paper addresses the conversion of Danish agricultural land from food/feed crops to energy crops. To this end, a life cycle inventory, which relates the input and output flows from and to the environment of 528 different crop systems, is built and described. This includes seven crops (annuals and perennials), two soil types (sandy loam and sand), two climate types (wet and dry), three initial soil carbon level (high, average, low), two time horizons for soil carbon changes (20 and 100 years), two residues management practices (removal and incorporation into soil) as well as three soil carbon turnover rate reductions in response to the absence of tillage for some perennial crops (0%, 25%, 50%). For all crop systems, nutrient balances, balances between above‐ and below‐ground residues, soil carbon changes, biogenic carbon dioxide flows, emissions of nitrogen compounds and losses of macro‐ and micronutrients are presented. The inventory results highlight Miscanthus as a promising energy crop, indicating it presents the lowest emissions of nitrogen compounds, the highest amount of carbon dioxide sequestrated from the atmosphere, a relatively high carbon turnover efficiency and allows to increase soil organic carbon. Results also show that the magnitude of these benefits depends on the harvest season, soil types and climatic conditions. Inventory results further highlight winter wheat as the only annual crop where straw removal for bioenergy may be sustainable, being the only annual crop not involving losses of soil organic carbon as a result of harvesting the straw. This, however, is conditional to manure application, and is only true on sandy soils.     

Adaptive evolution of drug targets in producer and non-producer organisms

MPA (mycophenolic acid) is an immunosuppressive drug produced by several fungi in Penicillium subgenus Penicillium. This toxic metabolite is an inhibitor of IMPDH (IMP dehydrogenase). The MPA-biosynthetic cluster of Penicillium brevicompactum contains a gene encoding a B-type IMPDH, IMPDH-B, which confers MPA resistance. Surprisingly, all members of the subgenus Penicillium contain genes encoding IMPDHs of both the A and B types, regardless of their ability to produce MPA. Duplication of the IMPDH gene occurred before and independently of the acquisition of the MPAbiosynthetic cluster. Both P. brevicompactum IMPDHs are MPA-resistant, whereas the IMPDHs from a non-producer are MPA-sensitive. Resistance comes with a catalytic cost: whereas P. brevicompactum IMPDH-B is >1000-fold more resistant to MPA than a typical eukaryotic IMPDH, its kcat/Km value is 0.5% of 'normal'. Curiously, IMPDH-B of Penicillium chrysogenum, which does not produce MPA, is also a very poor enzyme. The MPA-binding site is completely conserved among sensitive and resistant IMPDHs. Mutational analysis shows that the C-terminal segment is a major structural determinant of resistance. These observations suggest that the duplication of the IMPDH gene in the subgenus Penicillium was permissive for MPA production and that MPA production created a selective pressure on IMPDH evolution. Perhaps MPA production rescued IMPDH-B from deleterious genetic drift.     

Reference genome sequence of the model plant Setaria

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ～400-Mb assembly covers ～80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).     

A two-site lectinoenzymatic assay for determination of tumour marker glycoproteins in rectal secretions

A method is described for a titre-tray based two-site lectinoenzymatic assay of glycoproteins. WGA lectin, reacting with the core-part of glycans, was combined with lectins PNA and DBA, the latter two reacting with terminal parts of glycans. A standard curve was obtained with bovine submaxillary gland asialomucin, and measurements of human rectal secretion were calibrated against this curve. The assay showed an intra-assay reproducibility of 2.4–7.5%, and inter-assay reproducibility of 3.9–20.8% Recovery tests showed a linearity close to predicted values. The selected standard was ideal as inhibition of lectin binding by monosaccharides showed similar inhibition profiles for human rectal secretion and for asialomucin standard. Neuraminidase treatment dramatically increased the PNA binding to human rectal secretion immobilized on WGA. Western blotting of human rectal secretion demonstrated a large range of lectin-reactive glycoproteins, the main fraction reacting with all lectins being approximately 250 kDa. The assay described is well suited for studies of the glycan part of tumour marker glycoproteins, and changes occurring in these. It has a high sensitivity by ignoring that the glycans may be present on different molecules. Examination of rectal secretions from various cancer patients showed significantly increased PNA binding, as well as an increased PNA/DBA binding ratio, in patients with colorectal cancer (p<3×10-3) and, unexpectedly, in patients with other cancers (p<5×10-3). Abbreviations: HRS, human rectal secretion; PNA, peanut agglutinin; DBA, dolichos biflorus agglutinin; WGA, wheat germ agglutinin; BSA, bovine serum albumin; ELLSA, enzyme linked lectino-solid-phase assay; HRP, horseradish peroxidase; HRS: human rectal secretion; SDS, sodium dodecyl sulfate; PAGE, polyacrylamide gel electrophoresis; prot., protein; kDa, kilodalton; OPD, Ortho-phenylen-diamine; SA, Sialic acid; Gal, Galactose; GlcNAc, N-acetyl-D-glucosamine; GalNAc, N-acetyl-D-galactosamine; Fuc, fucose; Man, mannose; Glc, glucose This revised version was published online in November 2006 with corrections to the Cover Date.     

Molecular anatomy of the recombination mediator function of Saccharomyces cerevisiae Rad52

A helical filament of Rad51 on single-strand DNA (ssDNA), called the presynaptic filament, catalyzes DNA joint formation during homologous recombination. Rad52 facilitates presynaptic filament assembly, and this recombination mediator activity is thought to rely on the interactions of Rad52 with Rad51, the ssDNA-binding protein RPA, and ssDNA. The N-terminal region of Rad52, which has DNA binding activity and an oligomeric structure, is thought to be crucial for mediator activity and recombination. Unexpectedly, we find that the C-terminal region of Rad52 also harbors a DNA binding function. Importantly, the Rad52 C-terminal portion alone can promote Rad51 presynaptic filament assembly. The middle portion of Rad52 associates with DNA-bound RPA and contributes to the recombination mediator activity. Accordingly, expression of a protein species that harbors the middle and C-terminal regions of Rad52 in the rad52 Delta327 background enhances the association of Rad51 protein with a HO-made DNA double-strand break and partially complements the methylmethane sulfonate sensitivity of the mutant cells. Our results provide a mechanistic framework for rationalizing the multi-faceted role of Rad52 in recombination and DNA repair.     

An important role for type III interferon (IFN-lambda/IL-28) in TLR-induced antiviral activity

Type III IFNs (IFN-lambda/IL-28/29) are cytokines with type I IFN-like antiviral activities, which remain poorly characterized. We herein show that most cell types expressed both types I and III IFNs after TLR stimulation or virus infection, whereas the ability of cells to respond to IFN-lambda was restricted to a narrow subset of cells, including plasmacytoid dendritic cells and epithelial cells. To examine the role of type III IFN in antiviral defense, we generated IL-28Ralpha-deficient mice. These mice were indistinguishable from wild-type mice with respect to clearance of a panel of different viruses, whereas mice lacking the type I IFN receptor (IFNAR(-/-)) were significantly impaired. However, the strong antiviral activity evoked by treatment of mice with TLR3 or TLR9 agonists was significantly reduced in both IL-28RA(-/-) and IFNAR(-/-) mice. The type I IFN receptor system has been shown to mediate positive feedback on IFN-alphabeta expression, and we found that the type I IFN receptor system also mediates positive feedback on IFN-lambda expression, whereas IL-28Ralpha signaling does not provide feedback on either type I or type III IFN expression in vivo. Finally, using bone-marrow chimeric mice we showed that TLR-activated antiviral defense requires expression of IL-28Ralpha only on nonhemopoietic cells. In this compartment, epithelial cells responded to IFN-lambda and directly restricted virus replication. Our data suggest type III IFN to target a specific subset of cells and to contribute to the antiviral response evoked by TLRs.