Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2019
Authors
N. Feau Dario Isidro Ojeda Alayon S. Beauseigle G. J. Bilodeau A. Brar S. Cervantes-Arango A. L. Dale B. Dhillon C. Hammett P. Herath S. F. Shamoun C. K. M. Tsui P. Tanguay R. C. HamelinAbstract
Early detection provides the best way to prevent introduction and establishment of alien plant pathogens. Amplification of DNA by PCR has revolutionized the detection and monitoring of plant pathogens. Most of those assays rely on the amplification of a fraction of the genome of the targeted species. With the availability of whole genomes for a growing number of fungi and oomycetes it is becoming possible to compare genomes and discover regions that are unique to a target organism. This study has applied this pipeline to develop a set of hierarchical TaqMan real‐time PCR detection assays targeting DNA of all four Phytophthora ramorum lineages, and a closely related species, P. lateralis. Nine assays were generated: three targeting DNA of all P. ramorum lineages, one for each lineage of P. ramorum, one for P. lateralis and one targeting DNA of P. ramorum and P. lateralis. These assays were very accurate and sensitive, ranging from 98.7% to 100% detection accuracy of 2–10 gene copies of the targeted taxa from pure cultures or inoculated tissues. This level of sensitivity is within the lowest theoretical limit of detection of DNA. It is expected that these assays will be useful because of their high level of specificity and the ease with which they can be multiplexed because of the inherent flexibility in primer and probe design afforded by their lack of conservation in non‐target species.
Abstract
A robust hydrological modeling at a fine spatial resolution is a vital tool for Norway to simulate river discharges and hydrological components for climate adaptation strategies. However, it requires improvements of modelling methods, detailed observational data as input and expensive computational resources. This work aims to set up a distributed version of the HBV model with a physically based evapotranspiration scheme at 1 km resolution for mainland Norway and to calibrate/validate the model for 124 catchments using regionalized parameterizations. The Penman-Monteith equation was implemented in the HBV model and vegetation characteristics were derived from the Norwegian forest inventory combined with multi-source remote sensing data at 16 m spatial resolution. The estimated potential evapotranspiration (Ep) was compared with pan measurements and estimates from the MODerate Resolution Imaging Spectrometer (MOD16) products, the Global Land Evaporation Amsterdam Model (GLEAM) and Variable Infiltration Capacity (VIC) hydrological model. There are 5 climatic zones in Norway classified based on 4 temperature and precipitation indices. For each zone, the model was calibrated separately by optimizing a multi-objective function including the Nash-Sutcliff efficiency (NSE) and biases of selected catchments. In total, there are 85 catchments for calibration and 39 for validation. The Ep estimates showed good agreement with the measurements, GLEAM and VIC outputs. However, the MOD16 product significantly overestimates Ep compared to the other products. The discharge was well reproduced with the median daily NSE of 0.68/0.67, bias of −3%/−1%, Kling-Gupta efficiency (KGE) of 0.70/0.69 and monthly NSE of 0.80/0.78 in the calibration/validation periods. Our results showed a significant improvement compared to the previous HBV application for all catchments, with an increase of 0.08–0.16 in the median values of the daily NSE, KGE and monthly NSE. Both the temporal and spatial transferability of model parameterizations were also enhanced compared to the previous application.
Authors
Lampros LamprinakisAbstract
Purpose The purpose of this paper is to introduce the concept of embeddedness, highlight its connection with corporate social responsibility (CSR) strategies, and argue for its importance in securing and strengthening organizational resiliency. Design/methodology/approach Embeddedness and CSR are both well-researched topics but have been typically addressed on separate literature streams. The paper draws upon this diverse literature to introduce a conceptual framework for embeddedness in CSR. Findings The paper illustrates the importance of embeddedness and how it can enhance existing CSR strategies. A strongly embedded organization becomes deeply rooted on its socio-economic and natural environments, thus setting a symbiotic relationship that extends beyond any narrowly defined business purposes. Strong embeddedness has the potential to increase and further expand any CSR-related benefits while shielding the firm from economic downturns and thus increasing its resilience. Originality/value The paper builds upon CSR literature by incorporating the concept of embeddedness and then proposing how such an approach can strengthen an organization and increase its resilience.
Abstract
Utilisable crude protein (uCP), methane (CH4) production and other fermentation parameters were analysed in vitro for a diet in which grass silage was replaced by different levels of seaweed protein fractions prepared from three seaweed species: Saccharina latissima, Alaria esculenta and Palmaria palmata. Ten fractions from these three species in which the protein content had been increased and the salt content reduced by simple processing were tested, with inclusion levels in the diet based on the nitrogen content of the fractions. Following an extraction procedure, four fractions from Saccharina latissima, three from Alaria esculenta and one from Palmaria palmata, were gradually included in the diet by replacing high quality silage with approximately 0, 0.15, 0.30 and 0.45 g/g DM, while two high-protein fractions of Palmaria palmata were tested at replacement levels of 0, 0.075, 0.15 and 0.225 g/g DM. To estimate fermentation parameters, 500 mg of each diet were incubated in bottles with 60 mL buffered rumen fluid. Estimated uCP increased linearly with increasing replacement rate of grass silage with seaweed protein fractions (from 158 g/kg DM to 206 g/kg DM on average for all fractions). Increasing protein fraction from the brown seaweed Saccharina latissima in the diet significantly increased true organic matter digestibility (OMD) (from on average 0.786 to 0.821). Organic matter digestibility decreased with increasing level of Alaria esculenta fractions (from on average 0.785 to 0.733), which also gave a linear decrease in CH4 production (from on average 45.3 to 38.5 mL/g organic matter). As a result of decreased CH4 production and OMD, total volatile fatty acid concentration decreased with increasing level of Alaria esculenta fractions (from on average 69.5 to 63.0 mmol/L). Thus, positive and species-specific effects of seaweed on estimated uCP and fermentation parameters were observed in vitro when protein fractions remaining after an extraction procedure on seaweed partly replaced grass silage in the feed ration.
Abstract
Potato (Solanum tuberosum L.) is one of the most important crops grown in Norway, and virus-free plants are required for commercial potato production and for preservation of potato germplasm. The present study evaluates three in vitro therapies – meristem culture, cryotherapy, and chemotherapy combined with thermotherapy – to eliminate viruses from eight historically valuable potato cultivars belonging to the Norwegian potato germplasm. Potato virus Y, potato virus M, potato virus X and potato virus S were present in eight selected old potato cultivars due to long-term conservation in open field. Double-antibody sandwich enzyme-linked immunological assay (DAS-ELISA) and biological indicators were the standard tests used to confirm virus infection in our study. Six virus-free plants from four potato cultivars were obtained after meristem culture, and no virus-free potato cultivars were obtained after cryotherapy. Virus-free frequency for eight different potato cultivars after combining chemotherapy with thermotherapy varied from 36.4% to 100%, with single virus elimination rates of between 74.2% and 92.9%. Chemotherapy compared with thermotherapy was the most effective of the three in vitro therapies used in this study. Highly sensitive small RNA high-throughput sequencing (HTS) was used to evaluate the virus status of potato virus-free materials after virus eradication, and no virus was found, which was consistent with the results of DAS-ELISA and biological indicators. Small RNA HTS has been reported for the first time to evaluate the virus status after virus elimination and to control virus-free potato nuclear stocks.
Authors
Andre van Eerde Aniko Varnai John-Kristian Jameson Lisa Paruch Anders Moen Jan Haug Anonsen Piotr Chylenski Hege Særvold Steen Inger Heldal Ralph Bock Vincent Eijsink Jihong Liu ClarkeAbstract
Sustainable production of biofuels from lignocellulose feedstocks depends on cheap enzymes for degradation of such biomass. Plants offer a safe and cost‐effective production platform for biopharmaceuticals, vaccines and industrial enzymes boosting biomass conversion to biofuels. Production of intact and functional protein is a prerequisite for large‐scale protein production, and extensive host‐specific post‐translational modifications (PTMs) often affect the catalytic properties and stability of recombinant enzymes. Here we investigated the impact of plant PTMs on enzyme performance and stability of the major cellobiohydrolase TrCel7A from Trichoderma reesei, an industrially relevant enzyme. TrCel7A was produced in Nicotiana benthamiana using a vacuum‐based transient expression technology, and this recombinant enzyme (TrCel7Arec) was compared with the native fungal enzyme (TrCel7Anat) in terms of PTMs and catalytic activity on commercial and industrial substrates. We show that the N‐terminal glutamate of TrCel7Arec was correctly processed by N. benthamiana to a pyroglutamate, critical for protein structure, while the linker region of TrCel7Arec was vulnerable to proteolytic digestion during protein production due to the absence of O‐mannosylation in the plant host as compared with the native protein. In general, the purified full‐length TrCel7Arec had 25% lower catalytic activity than TrCel7Anat and impaired substrate‐binding properties, which can be attributed to larger N‐glycans and lack of O‐glycans in TrCel7Arec. All in all, our study reveals that the glycosylation machinery of N. benthamiana needs tailoring to optimize the production of efficient cellulases.
Authors
Zhichao Chen Yuxin Miao Junjun Lu Lan Zhou Yue Li Hongyan Zhang Weidong Lou Zheng Zhang Krzysztof Kusnierek Changhua LiuAbstract
Improving nitrogen (N) management of small-scale farming systems in developing countries is crucially important for food security and sustainable development of world agriculture, but it is also very challenging. The N Nutrition Index (NNI) is a reliable indicator for crop N status, and there is an urgent need to develop an effective method to non-destructively estimate crop NNI in different smallholder farmer fields to guide in-season N management. The eBee fixed-wing unmanned aerial vehicle (UAV)-based remote sensing system, a ready-to-deploy aircraft with a Parrot Sequoia+ multispectral camera onboard, has been used for applications in precision agriculture. The objectives of this study were to (i) determine the potential of using fixed-wing UAV-based multispectral remote sensing for non-destructive estimation of winter wheat NNI in different smallholder farmer fields across the study village in the North China Plain (NCP) and (ii) develop a practical strategy for village-scale winter wheat N status diagnosis in small scale farming systems. Four plot experiments were conducted within farmer fields in 2016 and 2017 in a village of Laoling County, Shandong Province in the NCP for evaluation of a published critical N dilution curve and for serving as reference plots. UAV remote sensing images were collected from all the fields across the village in 2017 and 2018. About 150 plant samples were collected from farmer fields and plot experiments each year for ground truthing. Two indirect and two direct approaches were evaluated for estimating NNI using vegetation indices (VIs). To facilitate practical applications, the performance of three commonly used normalized difference VIs were compared with the top performing VIs selected from 59 tested indices. The most practical and stable method was using VIs to calculate N sufficiency index (NSI) and then to estimate NNI non-destructively (R2 = 0.53–0.56). Using NSI thresholds to diagnose N status directly was quite stable, with a 57–59% diagnostic accuracy rate. This strategy is practical and least affected by the choice of VIs across fields, varieties, and years. This study demonstrates that fixed-wing UAV–based remote sensing is a promising technology for in-season diagnosis of winter wheat N status in smallholder farmer fields at village scale. The considerable variability in local soil conditions and crop management practices influenced the overall accuracy of N diagnosis, so more studies are needed to further validate and optimize the reported strategy and consecutively develop practical UAV remote sensing–based in-season N recommendation methods.
Abstract
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Authors
Liv Jorunn HindAbstract
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