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Extracellular DNA (eDNA) is a major constituent of the extracellular matrix of Pseudomonas aeruginosa biofilms and its release is regulated via pseudomonas quinolone signal (PQS) dependent quorum sensing (QS). By screening a P. aeruginosa transposon library to identify factors required for DNA release, mutants with insertions in the twin-arginine translocation (Tat) pathway were identified as exhibiting reduced eDNA release, and defective biofilm architecture with enhanced susceptibility to tobramycin. P. aeruginosa tat mutants showed substantial reductions in pyocyanin, rhamnolipid and membrane vesicle (MV) production consistent with perturbation of PQS-dependent QS as demonstrated by changes in pqsA expression and 2-alkyl-4-quinolone (AQ) production. Provision of exogenous PQS to the tat mutants did not return pqsA, rhlA or phzA1 expression or pyocyanin production to wild type levels. However, transformation of the tat mutants with the AQ-independent pqs effector pqsE restored phzA1 expression and pyocyanin production. Since mutation or inhibition of Tat prevented PQS-driven auto-induction, we sought to identify the Tat substrate(s) responsible. A pqsA::lux fusion was introduced into each of 34 validated P. aeruginosa Tat substrate deletion mutants. Analysis of each mutant for reduced bioluminescence revealed that the primary signalling defect was associated with the Rieske iron-sulfur subunit of the cytochrome bc1 complex. In common with the parent strain, a Rieske mutant exhibited defective PQS signalling, AQ production, rhlA expression and eDNA release that could be restored by genetic complementation. This defect was also phenocopied by deletion of cytB or cytC1. Thus, either lack of the Rieske sub-unit or mutation of cytochrome bc1 genes results in the perturbation of PQS-dependent autoinduction resulting in eDNA deficient biofilms, reduced antibiotic tolerance and compromised virulence factor production., Author summary Pseudomonas aeruginosa is a highly adaptable human pathogen responsible for causing chronic biofilm-associated infections. Biofilms are highly refractory to host defences and antibiotics and thus difficult to eradicate. The biofilm extracellular matrix incorporates extracellular DNA (eDNA). This stabilizes biofilm architecture and helps confer tolerance to antibiotics. Since mechanisms that control eDNA release are not well understood, we screened a P. aeruginosa mutant bank for strains with defects in eDNA release and discovered a role for the twin-arginine translocation (Tat) pathway that exports folded proteins across the cytoplasmic membrane. Perturbation of the Tat pathway resulted in defective biofilms susceptible to antibiotic treatment as a consequence of perturbed pseudomonas quinolone (PQS) signalling. This resulted in the failure to produce or release biofilm components including eDNA, phenazines and rhamnolipids as well as microvesicles. Furthermore, we discovered that perturbation of PQS signalling was a consequence of the inability of tat mutants to translocate the Rieske subunit of the cytochrome bc1 complex involved in electron transfer and energy transduction. Given the importance of PQS signalling and the Tat system to virulence and biofilm maturation in P. aeruginosa, our findings underline the potential of the Tat system as a drug target for novel antimicrobial agents.

This study aims to determine the influence of mill type and pellet wood composition on particle size and shape of milled wood. The size and shape characteristics of pellets comminuted using power plant roller mills were compared with those obtained by using laboratory-scale roller- and hammer mills. A 2D dynamic imaging device was used for particle characterization. It was shown that mill type has a significant impact on particle size but an almost negligible effect on the shape of milled wood. Comminution in the pilot plant using a Loesche roller mill requires less energy than using a hammer mill, but generates a larger fraction of coarse particles. The laboratory-scale roller mill provides comparable results with the power plant roller mill with respect to particle size and shape. The authors would like to acknowledge the financial support received from the Danish Strategic Research Council (Grant Nr. DSF-10-093956), DONG Energy, Vattenfall and HOFOR. We would also like to thank the Wood Sciences Laboratory at Technical University of Munich for the help with the pellets comminution in the laboratory-scale hammer mill to test the repeatability of our results. Jarl Wallden from LatGran and Kalju Erras from Heatlets are acknowledged for helping with the preparation of wood material before pelletization. The authors thank DTU Combustion and Harmful Emission Control group for fruitful discussions. Jayme Currie and Associate Professor Sunkyu Park are acknowledged for the article proof reading. peer-reviewed 2019-03-14

The concentration and type of free radicals from the decay (termination stage) of pyrolysis at slow and fast heating rates and at high temperatures (above 1000°C) in biomass char have been studied. A room-temperature electron spin resonance spectroscopy study was conducted on original wood, herbaceous biomass, holocelluloses, lignin and their chars, prepared at high temperatures in a wire mesh reactor, an entrained flow reactor, and a tubular reactor. The radical concentrations in the chars from the decay stage range up between 7·1016 and 1.5·1018 spins g−1. The results indicated that the biomass major constituents (cellulose, hemicellulose, lignin) had a minor effect on remaining radical concentrations compared to potassium and silica contents. The higher radical concentrations in the wheat straw chars from the decay stage of pyrolysis in the entrained flow reactor compared to the wood chars were related to the decreased mobility of potassium in the char matrix, leading to the less efficient catalytic effects of potassium on the bond-breaking and radical re-attachments. The high Si levels in the rice husk caused an increase in the char radical concentration compared to the wheat straw because the free radicals were trapped in a char consisting of a molten amorphous silica at heating rates of 103–104 K s−1. The experimental electron spin resonance spectroscopy spectra were analyzed by fitting to simulated data in order to identify radical types, based on g-values and line widths. The results show that at high temperatures, mostly aliphatic radicals (g = 2.0026–2.0028) and PAH radicals (g = 2.0027–2.0031) were formed. The authors would like to acknowledge the financial support that they received for this project from Danish Strategic Research Council (Grant Nr. DSF-10-093956), DONG Energy and Vattenfall. We also thank Professor Spliethoff and Markus Steibel (TU Munich) for the support with the entrained flow reactor experiments, Jesper Harholt (Carlsberg Laboratory) and Søren Talbro Barsberg (University of Copenhagen, Department of Geosciences and Natural Resource Management) for assisting with the biomass compositional analysis and for the fruitful discussions. peer-reviewed 2018-09-06

Monoclonal antibodies (mAbs) are widely used and powerful research tools, but the generation of mAbs against glycan epitopes is generally more problematic than against proteins. This is especially significant for research on polysaccharide-rich land plants and algae (Viridiplantae). Most antibody production is based on using single antigens, however, there are significant gaps in the current repertoire of mAbs against some glycan targets with low immunogenicity. We approached mAb production in a different way and immunised with a complex mixture of polysaccharides. The multiplexed screening capability of carbohydrate microarrays was then exploited to deconvolute the specificities of individual mAbs. Using this strategy, we generated a set of novel mAbs, including one against starch (INCh1) and one against ulvan (INCh2). These polysaccharides are important storage and structural polymers respectively, but both are generally considered as having limited immunogenicity. INCh1 and INCh2 therefore represent important new molecular probes for Viridiplantae research. Moreover, since the α-(1-4)-glucan epitope recognised by INCh1 is also a component of glycogen, this mAb can also be used in mammalian systems. We describe the detailed characterisation of INCh1 and INCh2, and discuss the potential of a non-directed mass-screening approach for mAb production against some glycan targets.

This study aims to provide a geometrical description of biomass particles that can be used in combustion models. The particle size of wood and herbaceous biomass was compared using light microscope, 2D dynamic imaging, laser diffraction, sieve analysis and focused beam reflectance measurement. The results from light microscope and 2D dynamic imaging analysis were compared and it showed that the data on particle width, measured by these two techniques, were identical. Indeed, 2D dynamic imaging was found to be the most convenient particle characterization method, providing information on both the shape and the external surface area. Importantly, a way to quantify all three dimensions of biomass particles has been established. It was recommended to represent a biomass particle in combustion models as an infinite cylinder with the volume-to-surface ratio (V/A) measured using 2D dynamic imaging. The authors would like to acknowledge the financial support received from the Danish Strategic Research Council (Grant Nr. DSF-10-093956), Kempestiftelse, DONG Energy, Vattenfall and HOFOR. We would like also to thank Ian Haley and Brian O’Sullivan from Mettler Toledo for assisting with FBRM measurements. The authors thank DTU Combustion and Harmful Emission Control group for the fruitful discussions. Erika Christ is acknowledged for the article proof reading. peer-reviewed 2019-06-29

This paper reviews strategies and methods to improve accuracies of genomic predictions from the perspective of a numerically small population. Improvements are realized by influencing one or both of the main factors: (1) improve or increase genomic connections to phenotypic records in training data. (2) Models and strategies to focus genomic predictions on markers closer to the causative variants. Combining populations into a joint reference population results in high improvements when combining populations of the same breed and diminishes as the genetic distance between populations increases. For distantly related breeds sophisticated Bayesian variable selection models in combination with denser markers sets or functional subsets of markers is needed. This is expected to be further improved by the efficient use of sequence information. In addition predictions can be improved by the use of phenotypes of genotyped and non-genotyped cows directly. For a small population the optimal approach will combine the above components.

This study presents the effect of biomass origin on the yield, nanostructure and reactivity of soot. Soot was produced from wood and herbaceous biomass pyrolysis at high heating rates and at temperatures of 1250 and 1400 °C in a drop tube furnace. The structure of solid residues was characterized by electron microscopy techniques, X-ray diffraction and N2 adsorption. The reactivity of soot was investigated by thermogravimetric analysis. Results showed that soot generated at 1400 °C was more reactive than soot generated at 1250 °C for all biomass types. Pinewood, beechwood and wheat straw soot demonstrated differences in alkali content, particle size and nanostructure. Potassium was incorporated in the soot matrix and significantly influenced soot reactivity. Pinewood soot particles produced at 1250 °C had a broader particle size range (27.2–263 nm) compared to beechwood soot (33.2–102 nm) and wheat straw soot (11.5–165.3 nm), and contained mainly multi-core structures. The authors at DTU would like to acknowledge the financial support that they received for this project from Danish Strategic Research Council (Grant No. DSF-10-093956), DONG Energy and Vattenfall. We also thank Professor Kenny Ståhl (DTU Chemistry) for assisting with XRD measurements and data processing, Professor Søren Talbro Barsberg (University of Copenhagen) for assisting with FTIR measurements and Dr. Martin Høj for assiting with N2 adsorption analysis. The A.P. Møller and Chastine Mc-Kinney Møller Foundation is acknowledged for their contribution toward the establishment of the Center for Electron Nanoscopy in the Technical University of Denmark and thanks to Wilhelmus Huyzer for initial TEM imaging. Kempe Foundation is acknowledged for the financial support to construct the DTF at LTU. Assistant Professor Catherine Brewer is acknowledged for the article proof reading. The authors acknowledge Professor Randy Vander Wal for the scientific discussions. peer-reviewed

SUMMARYEleven widely used crop simulation models (APSIM, CERES, CROPSYST, COUP, DAISY, EPIC, FASSET, HERMES, MONICA, STICS and WOFOST) were tested using spring barley (Hordeum vulgare L.) data set under varying nitrogen (N) fertilizer rates from three experimental years in the boreal climate of Jokioinen, Finland. This is the largest standardized crop model inter-comparison under different levels of N supply to date. The models were calibrated using data from 2002 and 2008, of which 2008 included six N rates ranging from 0 to 150 kg N/ha. Calibration data consisted of weather, soil, phenology, leaf area index (LAI) and yield observations. The models were then tested against new data for 2009 and their performance was assessed and compared with both the two calibration years and the test year. For the calibration period, root mean square error between measurements and simulated grain dry matter yields ranged from 170 to 870 kg/ha. During the test year 2009, most models failed to accurately reproduce the observed low yield without N fertilizer as well as the steep yield response to N applications. The multi-model predictions were closer to observations than most single-model predictions, but multi-model mean could not correct systematic errors in model simulations. Variation in soil N mineralization and LAI development due to differences in weather not captured by the models most likely was the main reason for their unsatisfactory performance. This suggests the need for model improvement in soil N mineralization as a function of soil temperature and moisture. Furthermore, specific weather event impacts such as low temperatures after emergence in 2009, tending to enhance tillering, and a high precipitation event just before harvest in 2008, causing possible yield penalties, were not captured by any of the models compared in the current study.

The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens. The data identified six previously unidentified CBMfamilies that targeted beta-glucans, beta-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize beta-glucans and beta-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose.

Fast pyrolysis of wood and straw was conducted in a drop tube furnace (DTF) and compared with corresponding data from a wire mesh reactor (WMR) to study the influence of temperature (1000–1400)°C, biomass origin (pinewood, beechwood, wheat straw, alfalfa straw), and heating rate (103 °C/s, 104 °C/s) on the char yield and morphology. Scanning electron microscopy (SEM), elemental analysis, and ash compositional analysis were applied to characterize the effect of operational conditions on the solid residues (char, soot) and gaseous products. The char yield from fast pyrolysis in the DTF setup was 3 to 7% (daf) points lower than in the WMR. During fast pyrolysis pinewood underwent drastic morphological transformations, whereas beechwood and straw samples retained the original porous structure of the parental fuel with slight melting on the surface. The particle size of Danish wheat straw char decreased in its half-width with respect to the parental fuel, whereas the alfalfa straw char particle size remained unaltered at higher temperatures. Soot particles in a range from 60 to 300 nm were obtained during fast pyrolysis. The soot yield from herbaceous fuels was lower than from wood samples, possibly due to differences in the content of lignin and resin acids. The authors from DTU would like to acknowledge the financial support that they received for this project from Danish Strategic Research Council (Contract 0603-00429B), DONG Energy, and Vattenfall. We also thank DTU CEN, Gert Beckmann (Retsch Company) and Kawnish Kirtania (LTU) for assisting with TEM/SEM microscopy and CAMSIZER XT measurements and micro GC measurements. peer-reviewed

Fast pyrolysis of wheat straw and rice husk was carried out in an entrained flow reactor at high-temperatures (1000–1500) °C. The collected char was analyzed using X-ray diffractometry, N2-adsorption, scanning electron microscopy, particle size analysis with CAMSIZER XT, 29Si and 13C solid-state nuclear magnetic resonance spectroscopy and thermogravimetric analysis to investigate the effect of inorganic matter on the char morphology and oxygen reactivity. The silicon compounds were dispersed throughout the turbostratic structure of rice husk char in an amorphous phase with a low melting temperature (≈730 °C), which led to the formation of a glassy char shell, resulting in a preserved particle size and shape of chars. The high alkali content in the wheat straw resulted in higher char reactivity, whereas the lower silicon content caused variations in the char shape from cylindrical to near-spherical char particles. The reactivities of pinewood and rice husk chars were similar with respect to oxidation, indicating less influence of silicon oxides on the char reactivity. The authors would like to acknowledge the financial support that they received for this project from Danish Strategic Research Council (Grant DSF-10-093956), DONG Energy and Vattenfall. We also thank Gert Beckmann (Retsch Company) for assisting with the reproducibility tests on CAMSIZER XT, Professor Kenny Ståhl (DTU Chemistry) and Sunday Chukwudi Okoro (DTU, Chemical Engineering) for support with the XRD measurements and data processing, Dr. Martin Høj (DTU, Chemical Engineering) for assisting with N2-adsorption analysis and Andrea Hartung (TU Munich) for the careful ash compositional analysis. We emphasize special thank you to Andreas Geißler, Simon Schatzmann and Benedikt Schels for their support during measurements on the entrained flow reactor. peer-reviewed

International audience; We present a novel method for constructing linear secret sharing schemes (LSSS) from linear error correcting codes and linear universal hash functions in a blackbox way. The main advantage of this new construction is that the privacy property of the resulting secret sharing scheme essentially becomes independent of the code we use, only depending on its rate. This allows us to fully harness the algorithmic properties of recent code constructions such as efficient encoding and decoding or efficient list-decoding. Choosing the error correcting codes and universal hash functions involved carefully, we obtain solutions to the following open problems: - A linear near-threshold secret sharing scheme with both linear time sharing and reconstruction algorithms and large secrets (i.e. secrets of size $\Omega(n)$). Thus, the computational overhead per shared bit in this scheme is *constant*. - An efficiently reconstructible robust secret sharing scheme for $n/3 \leq t < (1 - \epsilon) \cdot n/2$ corrupted players (for any constant $\epsilon > 0$) with shares of optimal size $O(1 + \lambda / n)$ and secrets of size $\Omega(n + \lambda)$, where $\lambda$ is the security parameter.

Ongoing intensification and specialisation of livestock production lead to increasing volumes of manure to be managed, which are a source of the greenhouse gases (GHGs) methane (CH 4) and nitrous oxide (N 2O). Net emissions of CH 4 and N 2O result from a multitude of microbial activities in the manure environment. Their relative importance depends not only on manure composition and local management practices with respect to treatment, storage and field application, but also on ambient climatic conditions. The diversity of livestock production systems, and their associated manure management, is discussed on the basis of four regional cases (Sub-Saharan Africa, Southeast Asia, China and Europe) with increasing levels of intensification and priorities with respect to nutrient management and environmental regulation. GHG mitigation options for production systems based on solid and liquid manure management are then presented, and potentials for positive and negative interactions between pollutants, and between management practices, are discussed. The diversity of manure properties and environmental conditions necessitate a modelling approach for improving estimates of GHG emissions, and for predicting effects of management changes for GHG mitigation, and requirements for such a model are discussed. Finally, we briefly discuss drivers for, and barriers against, introduction of GHG mitigation measures for livestock production. There is no conflict between efforts to improve food and feed production, and efforts to reduce GHG emissions from manure management. Growth in livestock populations are projected to occur mainly in intensive production systems where, for this and other reasons, the largest potentials for GHG mitigation may be found.

Asseng, S. et al., Crop models are essential tools for assessing the threat of climate change to local and global food production1. Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature2. Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 °C to 32 °C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each °C of further temperature increase and become more variable over space and time., We thank the Agricultural Model Intercomparison and Improvement Project and its leaders C. Rosenzweig from NASA Goddard Institute for Space Studies and Columbia University (USA), J. Jones from University of Florida (USA), J. Hatfield from United States Department of Agriculture (USA) and J. Antle from Oregon State University (USA) for support. We also thank M. Lopez from CIMMYT (Turkey), M. Usman Bashir from University of Agriculture, Faisalabad (Pakistan), S. Soufizadeh from Shahid Beheshti University (Iran), and J. Lorgeou and J-C. Deswarte from ARVALIS—Institut du Végétal (France) for assistance with selecting key locations and quantifying regional crop cultivars, anthesis and maturity dates and R. Raymundo for assistance with GIS. S.A. and D.C. received financial support from the International Food Policy Research Institute (IFPRI). C.S. was funded through USDA National Institute for Food and Agriculture award 32011-68002-30191. C.M. received financial support from the KULUNDA project (01LL0905L) and the FACCE MACSUR project (031A103B) funded through the German Federal Ministry of Education and Research (BMBF). F.E. received support from the FACCE MACSUR project (031A103B) funded through the German Federal Ministry of Education and Research (2812ERA115) and E.E.R. was funded through the German Science Foundation (project EW 119/5-1). M.J. and J.E.O. were funded through the FACCE MACSUR project by the Danish Strategic Research Council. K.C.K. and C.N. were funded by the FACCE MACSUR project through the German Federal Ministry of Food and Agriculture (BMEL). F.T., T.P. and R.P.R. received financial support from FACCE MACSUR project funded through the Finnish Ministry of Agriculture and Forestry (MMM); F.T. was also funded through National Natural Science Foundation of China (No. 41071030). C.B. was funded through the Helmholtz project ‘REKLIM—Regional Climate Change: Causes and Effects’ Topic 9: ‘Climate Change and Air Quality’. M.P.R. and P.D.A. received funding from the CGIAR Research Program on Climate Change, Agriculture, and Food Security (CCAFS). G.O’L. was funded through the Australian Grains Research and Development Corporation and the Department of Environment and Primary Industries Victoria, Australia. R.C.I. was funded by Texas AgriLife Research, Texas A&M University. E.W. and Z.Z. were funded by CSIRO and the Chinese Academy of Sciences (CAS) through the research project ‘Advancing crop yield while reducing the use of water and nitrogen’ and by the CSIRO-MoE PhD Research Program.