Extending Miscanthus cultivation with novel germplasm at six contrasting sites

The OPTIMISC project received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement No. 289159.Peer reviewedPublisher PD

Progress in upscaling Miscanthus biomass production for the European bio-economy with seed-based hybrids

Funded by UK's Biotechnology and Biological Sciences Research Council (BBSRC) Department for Environment, Food and Rural Affairs (DEFRA). Grant Number: LK0863 BBSRC strategic programme Grant on Energy Grasses & Bio-refining. Grant Number: BBS/E/W/10963A01 OPTIMISC. Grant Number: FP7-289159 WATBIO. Grant Number: FP7-311929 Innovate UK/BBSRC ‘MUST’. Grant Number: BB/N016149/1Peer reviewedPublisher PD

Direct nitrous oxide emissions from oilseed rape cropping - a meta-analysis

Oilseed rape is one of the leading feedstocks for biofuel production in Europe. The climate change mitigation effect of rape methyl ester (RME) is particularly challenged by the greenhouse gas (GHG) emissions during crop production, mainly as nitrous oxide (N2O) from soils. Oilseed rape requires high nitrogen fertilization and crop residues are rich in nitrogen, both potentially causing enhanced N2O emissions. However, GHG emissions of oilseed rape production are often estimated using emission factors that account for crop-type specifics only with respect to crop residues. This meta-analysis therefore aimed to assess annual N2O emissions from winter oilseed rape, to compare them to those of cereals and to explore the underlying reasons for differences. For the identification of the most important factors, linear mixed effects models were fitted with 43 N2O emission data points deriving from 12 different field sites. N2O emissions increased exponentially with N-fertilization rates, but interyear and site-specific variability were high and climate variables or soil parameters did not improve the prediction model. Annual N2O emissions from winter oilseed rape were 22% higher than those from winter cereals fertilized at the same rate. At a common fertilization rate of 200 kg N ha−1 yr−1, the mean fraction of fertilizer N that was lost as N2O-N was 1.27% for oilseed rape compared to 1.04% for cereals. The risk of high yield-scaled N2O emissions increased after a critical N surplus of about 80 kg N ha−1 yr−1. The difference in N2O emissions between oilseed rape and cereal cultivation was especially high after harvest due to the high N contents in oilseed rape's crop residues. However, annual N2O emissions of winter oilseed rape were still lower than predicted by the Stehfest and Bouwman model. Hence, the assignment of oilseed rape to the crop-type classes of cereals or other crops should be reconsidered

Influence of cutting height on biomass yield and quality of miscanthus genotypes

Abstract Commercially achieved biomass yields are often lower than those obtained in scientific plot trials and estimated by crop models. This phenomenon is commonly referred to as the ‘commercial yield gap’. It needs to be understood and managed to achieve the yield expectations that underpin business models. Cutting height at harvest is one of the key factors determining biomass yield and quality. This study quantifies the impacts of cutting heights of diverse genotypes with different morphologies and in years with contrasting weather conditions before and during harvest. Harvests were made in March 2015 and March 2018 of six diverse miscanthus genotypes planted as part of the ‘OPTIMISC project’ in 2013 near Stuttgart, Germany. Biomass yield, dry matter content and nutrient concentrations were analysed in four 10 cm fractions working upwards from the ground level and a fifth fraction with the shoot biomass higher than 40 cm. As stems are slightly tapered (i.e. diameter decreases slightly with increasing cutting height), it was hypothesized that low cutting may lead to yield gains, but that these may be associated with lower quality biomass with higher moisture and higher nutrient offtakes. We calculated average yield losses of 270 kg ha−1 (0.83%) with each 1 cm increase in cutting height up to 40 cm. Although whole shoot mineral concentrations were significantly influenced by both genotype and year interactions, total nitrogen (1.89 mg g−1), phosphorus (0.51 mg g−1), potassium (3.72 mg g−1) and calcium (0.89 mg g−1) concentrations did not differ significantly from the concentrations in the lower basal sections. Overall, cutting height had a limited influence on nutrient and moisture content. Therefore, we recommend that cutting is performed as low as is practically possible with the available machinery and local ground surface conditions to maximize biomass yield

Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T)

Microbial dissimilatory sulfate reduction is commonplace in many anaerobic environments, though few acidophilic bacteria are known to mediate this process. We report the 4.64-Mb draft genome of the type strain of the moderate acidophile Desulfosporosinus acididurans, which was isolated from acidic sediment in a river draining the Soufrière volcano, Montserrat

Peat and other organic soils under agricultural use in germany: Properties and challenges for classification

Under natural conditions, peatlands store large amounts of soil organic carbon (SOC). However, they are under threat due to drainage which leads to mineralisation of soil organic matter to carbon dioxide (CO2). This situation is especially severe in Germany, where more than 70 % of peat and other organic soils are used for agriculture. This study assessed the properties of these soils within the framework of the first German Agricultural Soil Inventory. In a nationwide 8 × 8 km grid, soils from a total of 3104 sites were sampled to depths of up to one metre or down to the peat base. Of these sites, 146 were on peat and other organic soils; and 31 % of the 146 sites were being affected not only by drainage but also by changes in horizonation (e.g. mineral covers, deep ploughing). The classification of heavily disturbed sites is limited within the German Manual of Soil Mapping, which has led to the development of an adapted classification scheme for peat and other organic soils under agricultural use in Germany. The respective peat classes showed distinct patterns of SOC and total nitrogen (Nt) contents and stocks, bulk density (BD) and C:N ratios. Overall, a SOC stock of 529 ± 201 t ha-1 and a Nt stock of 29.3 ± 13.9 t ha-1 were found within a depth of 0–100 cm. However, in deeper profiles, 48 % of the total SOC was stored below 100 cm depth down to the peat base. High SOC stocks were also found in peat-derived, mineral-covered and deep-ploughed organic soils, which might be classified as mineral soils depending on the classification system used but are still prone to mineralisation and need to be considered in terms of emissions reporting and mitigation. Logarithmic and quadratic pedotransfer functions were developed to estimate BD and SOC density, respectively, from SOC contents. This is necessary for the calculation of SOC stocks when analyses of BD are absent. The quadratic relationship between SOC content and SOC density clearly showed that heavily degraded organic soils store as much SOC in a defined volume as more natural ones, and that any estimates of differences in potential CO2 emissions should not be based on SOC content, but on SOC density instead

Genome Sequence of the Acidophilic Sulfate-Reducing Peptococcaceae Strain CEB3

We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one of the very few reported acidophilic sulfate-reducing isolates. The 5.04-Mb draft genome harbors 5,069 predicted protein-encoding and 66 RNA genes

From predicting to analyzing {HIV}-1 resistance to broadly neutralizing antibodies

Treatment with broadly neutralizing antibodies (bNAbs) has recently proven effective against HIV-1 infections in humanized mice, non-human primates, and humans. For optimal treatment, susceptibility of the patient’s viral strains to a particular bNAb has to be ensured. Since no computational approaches are so far available, susceptibility can only be tested in expensive and time-consuming neutralization experiments. Here, we present well-performing computational models (AUC up to 0.84) that can predict HIV-1 resistance to bNAbs given the envelope sequence of the virus. Having learnt important binding sites of the bNAbs from the envelope sequence, the models are also biologically meaningful and useful for epitope recognition. Additional to the prediction result, we provide a motif logo that displays the contribution of the pivotal residues of the test sequence to the prediction. As our prediction models are based on non-linear kernels, we introduce a new visualization technique to improve the model interpretability. Moreover, we confirmed previous experimental findings that there is a trend towards antibody resistance for the subtype B population of the virus. While previous experiments considered rather small and selected cohorts, we were able to show a similar trend for the global HIV-1 population comprising all major subtypes by predicting the neutralization sensitivity for around 36,000 HIV-1 sequences- a scale-up which is very difficult to achieve in an experimental setting

CD47 Expression Defines Efficacy of Rituximab with CHOP in Non-Germinal Center B-cell (Non-GCB) Diffuse Large B-cell Lymphoma Patients (DLBCL), but Not in GCB DLBCL

Addition of rituximab (R) to "CHOP" (cyclophosphamide, doxorubicin, vincristine, and prednisone) chemotherapy improved outcome for diffuse large B-cell lymphoma (DLBCL) patients. Approximately 40% of patients who receive R-CHOP still succumb to disease due to intrinsic resistance or relapse. A potential negative regulator of DLBCL treatment outcome is the CD47 "don't eat me" immune checkpoint. To delineate the impact of CD47, we used a clinically and molecularly well-annotated cohort of 939 DLBCL patients, comprising both germinal center B-cell (GCB) and non-GCB DLBCL subtypes, treated with either CHOP or R-CHOP. High (above median) CD47 mRNA expression correlated with a detrimental effect on overall survival (OS) when DLBCL patients received R-CHOP therapy (P = 0.001), but not CHOP therapy (P = 0.645). Accordingly, patients with low CD47 expression benefited most from the addition of rituximab to CHOP [HR, 0.32; confidence interval (CI), 0.21-0.50; P <0.001]. This negative impact of high CD47 expression on OS after R-CHOP treatment was only evident in cancers of non-GCB origin (HR, 2.09; CI, 1.26-3.47; P = 0.004) and not in the GCB subtype (HR, 1.16; CI, 0.68-1.99; P = 0.58). This differential impact of CD47 in non-GCB and GCB was confirmed in vitro, as macrophage-mediated phagocytosis stimulated by rituximab was augmented by CD47-blocking antibody only in non-GCB cell lines. Thus, high expression of CD47 mRNA limited the benefit of addition of rituximab to CHOP in non-GCB patients, and CD47-blockade only augmented rituximab-mediated phagocytosis in non-GCB cell lines. Patients with non-GCB DLBCL may benefit from CD47-targeted therapy in addition to rituximab

Dual inhibition of histone deacetylases and phosphoinositide 3-kinase enhances therapeutic activity against B cell lymphoma

Phosphoinositide 3-kinase (PI3K) and Myc are known to cooperate in promoting the survival and growth of a variety of B-cell lymphomas. While currently there are no small molecule inhibitors of Myc protein, histone deacetylase (HDAC) inhibitors have been shown to reduce levels of Myc protein by suppressing its transcription. We assessed the efficacy of CUDC-907, a new rationally designed dual inhibitor of PI3K and HDACs, in a panel of lymphoma cell lines. CUDC-907 treatment resulted in a dose- and time-dependent growth inhibition and cell death of DLBCL cell lines, irrespective of the cell of origin. CUDC-907 treatment down-regulated the phosphorylation of PI3K downstream targets, including AKT, PRAS40, S6, and 4EBP1, increased histone 3 acetylation, and decreased Myc protein levels. SILAC-based quantitative mass spectrometry demonstrated that CUDC-907 treatment decreased the protein levels of several components of the B cell receptor (BCR) and Toll like receptor (TLR) pathways, including BTK, SYK, and MyD88 proteins. These cellular changes were associated with an inhibition of NF-kB activation. CUDC-907 demonstrated in vivo efficacy with no significant toxicity in a human DLBCL xenograft mouse model. Collectively, these data provide a mechanistic rationale for evaluating CUDC-907 for the treatment of patients with Myc and PI3K-dependent lymphomas