Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Optimum strip width increases dry matter, nutrient accumulation, and seed yield of intercrops under the relay intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khan, Imran ; Khan, Ahsin ; Din, Atta Mohi Ud ; Naeem, Muhammd ; Meraj, Tehseen Ahmad ; Hassan, Muhammad Jawad ; Khan, Aaqil ; Lu, Feng Zhi ; Liu, Xin ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2020
    Food and Energy Security 9 (2020)2. - ISSN 2048-3694
    competition ratio - growing space - maize - relay intercropping - soybean

    Strip width management is a critical factor for producing higher crop yields in relay intercropping systems. A 2-year field experiment was carried out during 2012 and 2013 to evaluate the effects of different strip width treatments on dry-matter production, major-nutrient (nitrogen, phosphorus, and potassium) uptake, and competition parameters of soybean and maize in relay intercropping system. The strip width (SW) treatments were 0.40, 0.40, and 0.40 m (SW1); 0.40, 0.40, and 0.50 m (SW2); 0.40, 0.40, and 0.60 m (SW3); and 0.40, 0.40, and 0.70 m (SW4) for soybean row spacing, maize row spacing, and spacing between soybean and maize rows, respectively. As compared to sole maize (SM) and sole soybean (SS), relay-intercropped maize and soybean accumulated lower quantities of nitrogen, phosphorus, and potassium in all treatments. However, maize in SW1 accumulated higher nitrogen, phosphorus, and potassium than SW4 (9%, 9%, and 8% for nitrogen, phosphorus, and potassium, respectively). Soybean in SW3 accumulated 25% higher nitrogen, 33% higher phosphorus, and 24% higher potassium than in SW1. The improved nutrient accumulation in SW3 significantly increased the soybean dry matter by 19%, but slightly decreased the maize dry matter by 6% compared to SW1. Similarly, SW3 increased the competition ratio value of soybean (by 151%), but it reduced the competition ratio value of maize (by 171%) compared to SW1. On average, in SW3, relay-cropped soybean produced 84% of SS seed yield and maize produced 98% of SM seed yield and achieved the land equivalent ratio of 1.8, demonstrating the highest level in the world. Overall, these results suggested that by selecting the appropriate strip width (SW3; 0.40 m for soybean row spacing, 0.40 m maize row spacing, and 0.60 m spacing between soybean and maize rows), we can increase the nutrient uptake (especially nitrogen, phosphorus, and potassium), dry-matter accumulation, and seed yields of relay-intercrop species under relay intercropping systems.

    A suppressor of axillary meristem maturation promotes longevity in flowering plants
    Karami, Omid ; Rahimi, Arezoo ; Khan, Majid ; Bemer, Marian ; Hazarika, Rashmi R. ; Mak, Patrick ; Compier, Monique ; Noort, Vera van; Offringa, Remko - \ 2020
    Nature Plants 6 (2020)4. - ISSN 2055-026X - p. 368 - 376.

    Post-embryonic development and longevity of flowering plants are, for a large part, determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. The genes that are associated with AM maturation and underlie the differences between monocarpic (reproduce once and die) annual and the longer-lived polycarpic (reproduce more than once) perennial plants are still largely unknown. Here we identify a new role for the ArabidopsisAT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) gene as a suppressor of AM maturation. Loss of AHL15 function accelerates AM maturation, whereas ectopic expression of AHL15 suppresses AM maturation and promotes longevity in monocarpic Arabidopsis and tobacco. Accordingly, in Arabidopsis grown under longevity-promoting short-day conditions, or in polycarpic Arabidopsis lyrata, expression of AHL15 is upregulated in AMs. Together, our results indicate that AHL15 and other AHL clade-A genes play an important role, directly downstream of flowering genes (SOC1, FUL) and upstream of the flowering-promoting hormone gibberellic acid, in suppressing AM maturation and extending the plant’s lifespan.

    Effect of arginine or glutamine supplementation and milk feeding allowance on small intestine development in calves
    Keulen, P. van; Khan, M.A. ; Dijkstra, J. ; Knol, F. ; McCoard, S.A. - \ 2020
    Journal of Dairy Science 103 (2020)5. - ISSN 0022-0302 - p. 4754 - 4764.
    L-arginine - L-glutamine - milk allowance - small intestine development

    The development of the small intestine (SI) is important for the health and growth of neonatal calves. This study evaluated the effect of arginine (Arg) and glutamine (Gln) supplementation and 2 levels of milk allowance on the histomorphological development of the SI in preweaning calves. Sixty mixed-sex Friesian × Jersey calves (3–5 d of age) were offered reconstituted whole milk (125 g/L, 26% fat, 26% protein) at either high (20% of arrival body weight/d; HM) or low (10% of arrival body weight/d; LM) milk allowance without (Ctrl) or with supplementary Arg or Gln (at 1% of milk dry matter) in a 2 × 3 factorial design (n = 10/treatment). After 35 d on the diets, all calves were slaughtered to collect tissues for examination of SI development. Calves in the HM group had higher milk intake, total weight gain, and average daily gain compared with LM calves, but no effect of AA supplementation nor an interaction between milk allowance and AA supplementation was observed. For the duodenum, we observed an AA by milk allowance interaction for villus height and width, and goblet cell number per villus (HM-Arg > HM-Gln > HM-Ctrl), and villus height to crypt depth ratio (HM-Arg > HM-Gln = HM-Ctrl), but no effect of AA supplementation in the LM group. Goblet cell numbers per 100 μm of SI were greater in Arg-supplemented calves than in unsupplemented controls, with Gln-supplemented calves intermediate to but not different from the other groups. Epithelium thickness was greater in LM than in HM calves. Villus density, crypt depth, and muscle thickness did not differ between groups. For the jejunum, there was an AA by milk allowance interaction for villus height, villus surface area, and villus height to crypt depth ratio (HM-Arg = HM-Gln > HM-Ctrl), with no effect of AA supplementation in the LM groups. Amino acid supplementation affected goblet cell number per villus (HM-Gln > HM-Ctrl calves, HM-Arg intermediate), and both LM-Arg and LM-Gln calves had greater numbers than LM-Ctrl calves. Villus width, crypt depth, and muscle thickness were greater in HM than LM calves but there was no effect of AA supplementation. Villus density, goblet cell number per 100 μm of SI, and epithelium thickness were unaffected by AA supplementation and milk allowance. Milk allowance and AA supplementation had no effect on SI morphology in the ileum. Increasing milk allowance improved villus height, width, and surface area but only in Arg- or Gln-supplemented calves, not in control calves. The observed changes in development may be important for intestinal functionality, integrity, and barrier function in preweaning calves, potentially through increased cell growth and proliferation or reduced levels of cellular atrophy.

    Chemical composition, ruminal degradation kinetics and methane production (In vitro) potential of local and exotic grass species grown in Peshawar
    Khan, Nazir Ahmad ; Rahman, Sadeeq U.R. ; Cone, John W. - \ 2020
    Pakistan Journal of Botany 52 (2020)1. - ISSN 0556-3321 - p. 161 - 166.
    In vitro gas production - Methane emission - Nutritive value - Rumen fermentation - Tropical grass species

    Livestock production, and small scale and extensive grazing livestock production systems in Pakistan lack long-term sustainability due to declining quantity and quality of green forages and pastures. Information on the nutritional value of range/pasture and cultivated grass species is required to design proper strategies not only for nutritional management of grazing animals, but also for development of good quality forage resources. Therefore, the current study was planned to: (i) analyze the chemical profile of traditional and novel grasses grown in Peshawar; (ii) quantify the methane emission potential of the grass species; and (iii) quantify the differences among species in thei r nutritive value and methane emission. Ten grass species, namely, Sudex (Sorghum × sudangrass), Jumbo grass (Sorghum bicolour× Sorghum sudanefe), Sorghum almum, Pennisetum purpureum, Vetiveria zizanioides, Panicum colaratum, Cynodon dactylon, Bothriochloa pertusa, Splenda setaria and Desmostachya bipinnata were evaluated under uniform agronomic and environmental conditions. The results showed that the contents of all measured chemical components, mineral profile (except Zn), In vitro digestibility of dry matter (DMD), and In vitro gas (GP) and methane-production had large variation among the grass species. Among the grasses, Jumbo grass had greater CP (11.9% DM) content and In vitro DMD (65.9% DM), and produced greater amount of total gas, that contained lowest proportion of methane. In contrast, D. bipinnata had lowest contents of CP (6.3% DM) and In vitro DMD (43.7% DM), and produced lower amount of total gas, with highest proportion methane in total GP. Next to D. bipinnata, V. zizanioides had lower degradability/GP and highest proportion of methane in total gas. The large variation in chemical composition, DMD and methane-emission potential of the summer grass species presents a prospect to select and further develop grass species that have lower methane-emission potential and high nutritional value. Further research is needed to investigate the changes in chemical profile, DMD and methane-emission of forage species between seasons and with maturity.

    Multi-stakeholder participation for sustainable delta management: a challenge of the socio-technical transformation in the management practices in Bangladesh
    Mutahara, M. ; Warner, J.F. ; Khan, M.S.A. - \ 2020
    International Journal of Sustainable Development and World Ecology (2020). - ISSN 1350-4509
    community - delta - multi-stakeholder processes - participation - sustainability - Tidal River Management - transformation - water-logging

    In Bangladesh, participation discourse has officially become part of the objectives of the government and international agencies for water management projects since the mid-1990s. At the same historical timeframe, originating from indigenous knowledges Tidal River Management (TRM) has been formalized as a less structural and more natural management intervention to prevent the severe water-logging in the South-west region in the Bangladesh delta. It theoretically constituted a form of participation in the delta management system involving local community groups with government and management authorities. However, multi-stakeholder participation is still very challenging in practices. Even community management approaches are not sustained in delta management practices in Bangladesh. In this research, a socio-technical transformation is defined through a participatory research in the south-west coastal area having both qualitative and quantitative evaluation of changes in the delta management system brought about by TRM practices. This article also analyses the current problems besetting organized community participation in existing management practices and suggests the ways of developing effective multi-stakeholder processes (MSPs) with respect to sustainable management goal in deltas.

    Efficient oxidation and adsorption of As(III) and As(V) in water using a Fenton-like reagent, (ferrihydrite)-loaded biochar
    Huang, Yifan ; Gao, Minling ; Deng, Yingxuan ; Khan, Zulqarnain Haider ; Liu, Xuewei ; Song, Zhengguo ; Qiu, Weiwen - \ 2020
    Science of the Total Environment 715 (2020). - ISSN 0048-9697
    Aadsorption - Bbiochar - Fferrihydrite - Iinorganic arsenic - Mmechanism - Ooxidation

    The by-product of the traditional Fenton reaction, colloidal arsenic-‑iron oxide, is migratable and may cause secondary environmental pollution. This paper reported a new strategy involving oxidizing and immobilizing inorganic arsenic using the Fenton reaction, and avoiding the risk of secondary contamination. Lab synthesized ferrihydrite-loaded biochar (FhBC) was developed for oxidizing and binding As(III) and As(V) in aqueous solution. Batch experiments and a series of spectrum analysis (e.g., X-ray photoelectron spectroscopy [XPS], electron paramagnetic resonance [EPR], and Fourier transform infrared spectroscopy [FTIR]) were conducted to study the oxidizing or adsorption capacity and mechanism. The maximum adsorption capacity of FhBC for As(III) and As(V) is 1.315 and 1.325 mmol/g, respectively. In addition, FhBC has an efficient oxidizing capacity within a wide pH range, which is because biochar promotes the Fenton reaction by acting as an electron donator, electron shuttler, or by providing persistent free radicals. Moreover, the adsorption mechanism was studied by FTIR spectroscopy, XPS, and X-ray diffraction (XRD). The formation of internal spherical complexes and iron oxides with a higher degree of crystallization was observed, which indicate that the products of adsorption are stable and robust in a complex environment and can exist in a highly crystallized form after adsorbing arsenic ions. Therefore, the use of FhBC as an adsorbent for arsenic represents a new strategy of using the Fenton reaction while reducing secondary contamination. These results may contribute to further mechanistic studies or extensive practical applications of FhBC.

    Institutional arrangements for the Delta Centre
    Terwisscha van Scheltinga, Catharien ; Khan, Shah Alam ; Khan, Abu Saleh ; Zevenbergen, Chris - \ 2019
    Infrastructure for Innovative Research on Healthy Food Choice, Preparation and Consumption: A Position Paper on the RICHFIELDS project
    Seljak, Barbara Korousic ; Poppe, Krijn ; Finglas, Paul ; Timotijevic, Lada ; Veer, Pieter van 't; Zimmerman, Karin - \ 2019
    In: Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019. - Institute of Electrical and Electronics Engineers Inc. (Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019 ) - ISBN 9781728108582 - p. 5183 - 5185.
    consumer - data - food choice - interoperability - nutrition

    This paper presents the recently finished EU-funded RICHFIELDS project aimed to design a new research infrastructure that would foster research in the areas of food and nutrition with a focus on consumers' behavior and lifestyle. In this project, an architecture of a new consumer data platform was designed and discussed from the researchers, business, management, ethical and legal points of view. Also new methodology for supporting big and open data standardization and interoperability was developed.

    Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds
    Wilhelmsson, Per K.I. ; Chandler, Jake O. ; Fernandez-Pozo, Noe ; Graeber, Kai ; Ullrich, Kristian K. ; Arshad, Waheed ; Khan, Safina ; Hofberger, Johannes ; Buchta, Karl ; Edger, Patrick P. ; Pires, J.C. ; Schranz, Eric ; Leubner-Metzger, Gerhard ; Rensing, Stefan A. - \ 2019
    Wageningen University and Research
    Aethionema arabicum - Dimorphic seeds - Reference and reference-free - RNA-seq - Transciptome
    Background RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy â producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). Results A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. Conclusions Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.
    Automatic Detection of Tulip Breaking Virus (TBV) Using a Deep Convolutional Neural Network
    Polder, Gerrit ; Westeringh, Nick Van De ; Kool, Janne ; Khan, Haris Ahmad ; Kootstra, Gert ; Nieuwenhuizen, Ard - \ 2019
    IFAC-PapersOnLine 52 (2019)30. - ISSN 2405-8963 - p. 12 - 17.
    Tulip crop production in the Netherlands suffers from severe economic losses caused by virus diseases such as the Tulip Breaking Virus (TBV). Infected plants which can spread the disease by aphids must be removed from the field as soon as possible. As the availability of human experts for visual inspection in the field is limited, there is an urgent need for a rapid, automated and objective method of screening. From 2009-2012, we developed an automatic machine-vision-based system, using classical machine-learning algorithms. In 2012, the experiment conducted a tulip field planted at production density of 100 and 125 plants per square meter, resulting in images with overlapping plants. Experiments based on multispectral images resulted in scores that approached results obtained by experienced crop experts. The method, however, needed to be tuned specifically for each of the data trails, and a NIR band was needed for background segmentation. Recent developments in artificial intelligence and specifically in the area of convolutional neural networks, allow the development of more generic solutions for the detection of TBV. In this study, a Faster R-CNN network is applied on part of the data from the 2012 experiment. The outcomes show that the results are almost the same compared to the previous method using only RGB data.
    Optimum leaf defoliation: A new agronomic approach for increasing nutrient uptake and land equivalent ratio of maize soybean relay intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khan, Imran ; Hassan, Muhammad Jawad ; Ansar, Muhammad ; Chen, Yuan Kai ; Xi, Zeng Jin ; Shi, Jian Yi ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2019
    Field Crops Research 244 (2019). - ISSN 0378-4290
    Defoliation - Economics - LER - Nutrient - Relay-intercropping

    Upper canopy leaves of maize decrease the light-transmittance at middle-strata-leaves of maize and soybean canopy in maize-soybean relay-intercropping systems (MS). This affects the uptake of nutrients and distribution patterns in various plant organs of intercrop species in MS. Judicious defoliation of maize plants in MS could help to alleviate this problem and improve nutrient uptake and intercrop yields. In a two-year field experiment with MS, including the measurements of biomass production, nutrients uptake, and distribution at the organ level, and grain yields of intercrop species, maize plants were subjected to four-leaf defoliation treatments to improve the light-transmittance of maize and soybean plants. Defoliation of the topmost two-leaves (T2), four-leaves (T4), six-leaves (T6) was compared to no defoliation (T0). Compared to T0, treatment T2 improved the uptake of nitrogen (N), phosphorus (P), and potassium (K) in each plant part of maize by 23, 12, and 11% (grain), 22, 19, and 13% (straw), and 28, 14, and 18% (root), respectively. Defoliation also enhanced the uptake of N, P, and K in each plant part of soybean by 5, 5, and 10% (grain), 10, 17, and 13% (straw), and 14, 11, and 11% (root), respectively. The improved nutrient uptake in T2 increased the total biomass and its distribution in the root, straw, and grain of soybean and maize by 15 and 13%, and 21 and 15%, 20 and 14%, 7 and 10%, respectively compared to T0. On average, over two years, under T2, relay-cropped maize obtained 107% of the sole-yield, and relay-cropped soybean obtained 65% of the sole-yield. The T2 defoliation treatment also achieved the highest land equivalent ratio of 1.69 and 1.77, with a net profit of 1301.6 $ ha−1 and 1293.4 $ ha−1 in 2017 and 2018, respectively. Following the optimum defoliation treatment of maize in maize-soybean intercrops, i.e., defoliation of the topmost two-leaves, the nutrient uptake can be increased, and the nutrient partitioning over plant organs be better balanced. Optimum defoliation, therefore, enhances the productivity of maize-soybean intercropping systems.

    A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. II. Tuber bulking and resource use efficiency
    Khan, Muhammad Sohail ; Yin, Xinyou ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Struik, Paul C. - \ 2019
    Field Crops Research 242 (2019). - ISSN 0378-4290
    Genotype-by-environment interaction - Heritability - Maturity type - Path coefficient analysis - QTL mapping

    Quantitative differences in tuber bulking of 100 genotypes in a segregating F1 population, their parents (SH, RH) and five contrasting cultivars of potato (Solanum tuberosum) grown in six environments were analysed using a piece-wise expolinear function. Tuber bulking was characterised by three parameters: cm, ED and wmax, where cm and ED were growth rate and effective duration, respectively, of the linear phase of tuber bulking, and wmax was the final tuber dry weight at the end of the linear phase (tE). We also analysed radiation (RUET) and nitrogen use efficiency (NUET), and their relationships with the model parameters. Values of cm and RUET were highest for early-maturing genotypes. Late-maturing genotypes had largest ED and NUET. As a result, wmax was higher in late genotypes than in early genotypes. Most traits exhibited high heritability and high genetic correlations with wmax. Path analysis showed that RUET, cm and a previously quantified parameter for total canopy cover Asum, had a major influence on wmax. Sixteen QTLs were detected for all traits explaining the phenotypic variance by up to 66%. One particular QTL on paternal linkage group V was detected for all traits with a major additive effect and maximum total phenotypic variance. Additional QTLs mostly associated with RH (cm, tE and ED) or both SH-RH linkage groups (NUET, wmax). Our study demonstrates that there are opportunities for improving tuber dry matter yield by selecting an optimal combination of important physiological traits.

    Maize leaf-removal: A new agronomic approach to increase dry matter, flower number and seed-yield of soybean in maize soybean relay intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khalid, Muhammad Hayder Bin ; Chen, Yuan Kai ; Wasaya, Allah ; Ahmed, Shoaib ; Ud Din, Atta Mohi ; Khan, Ahsin ; Ahmed, Saeed ; Yang, Feng ; Yang, Wenyu - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 1 p.

    Shading conditions adversely affect flower-number and pod-number of soybeans under maize-soybean relay-intercropping (MSR). Here we reveal that leaf-removal from maize-canopy improves the photosynthetically active radiation (PAR) transmittance and dry-matter production (DMP) of soybean (especially during the co-growth phase), and compensates the maize seed-yield loss by considerably increasing soybean seed-yield. In a two-year experiment with MSR, maize-plants were subjected to different leaf-removal treatments to increase the PAR-transmittance of soybean; removal of the topmost two-leaves (R2), four-leaves (R4), six-leaves (R6), with no-removal of leaves (R0). Leaf-removal treatments improved the PAR-transmittance, photosynthetic-rate, and morphological-characteristics of soybean under MSR. At 90 days after sowing, the dry-matter of pods, and seeds was increased by 25%, and 32%, respectively under R6 than R0. Importantly, enhanced PAR-transmittance and DMP under R6 enabled soybean to initiate a greater number of flowers 182.2 plant-1 compared to 142.7 plant-1 under R0, and it also decreased the flower-abscission (by 13%, from 54.9% under R0 to 47.6% under R6). These positive responses increased the pod-number by 49% and seed-number by 28% under R6 than R0. Overall, under R6, relay-intercropped soybean produced 78% of sole-soybean seed-yield, and relay-intercropped maize produced 81% of sole-maize seed-yield and achieved the land equivalent ratio of 1.59.

    Circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands, 2006-2016
    Bergervoet, Saskia A. ; Pritz-Verschuren, Sylvia B.E. ; Gonzales, Jose L. ; Bossers, Alex ; Poen, Marjolein J. ; Dutta, Jayeeta ; Khan, Zenab ; Kriti, Divya ; Bakel, Harm van; Bouwstra, Ruth ; Fouchier, Ron A.M. ; Beerens, Nancy - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 1 p.

    In this study, we explore the circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands. Surveillance data collected between 2006 and 2016 was used to evaluate subtype diversity, spatiotemporal distribution and genetic relationships between wild bird and poultry viruses. We observed close species-dependent associations among hemagglutinin and neuraminidase subtypes. Not all subtypes detected in wild birds were found in poultry, suggesting transmission to poultry is selective and likely depends on viral factors that determine host range restriction. Subtypes commonly detected in poultry were in wild birds most frequently detected in mallards and geese. Different temporal patterns in virus prevalence were observed between wild bird species. Virus detections in domestic ducks coincided with the prevalence peak in wild ducks, whereas virus detections in other poultry types were made throughout the year. Genetic analysis of the surface genes demonstrated that most poultry viruses were related to locally circulating wild bird viruses, but no direct spatiotemporal link was observed. Results indicate prolonged undetected virus circulation and frequent reassortment events with local and newly introduced viruses within the wild bird population. Increased knowledge on LPAI virus circulation can be used to improve surveillance strategies.

    Narrow-wide-row planting pattern increases the radiation use efficiency and seed yield of intercrop species in relay-intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Cai, Gao Ren ; Khalid, Muhammad Hayder Bin ; Iqbal, Nasir ; Hassan, Muhammad Jawad ; Meraj, Tehseen Ahmad ; Naeem, Muhammd ; Khan, Imran ; Ur Rehman, Sana ; Ansar, Muhammad ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2019
    Food and Energy Security 8 (2019)3. - ISSN 2048-3694
    competition - intercropping - land equivalent ratio - radiation use efficiency

    Planting arrangements affect radiation use efficiency (RUE) and competitiveness of intercrop species in intercropping systems. Here, we reveal that narrow-wide-row planting arrangement in maize-soybean relay-intercropping system increases the dry matter and competitiveness of soybean, increased the RUE of maize and soybean, and compensates the yield loss of maize by substantially increasing the yield of soybean. In this field study, maize was planted with soybean in different planting arrangements (P1, 20:180, P2, 40:160; P3, 60:140, and P4, 80:120) of relay intercropping, all the relay-intercropping treatments were compared with sole crops of maize (SM) and soybean (SS). Results showed that P1 improved the total RUE 3.26 g/MJ (maize RUE + soybean RUE) of maize and soybean in relay-intercropping system. Compared to P4, treatment P1 increased the soybean competition ratio (CR) values (by 55%) but reduced the maize CR values (by 29%), which in turn significantly improved the yield of soybean by maintaining the maize yield. Generally, in P1, soybean produced 82% of SS yield, and maize produced 88% of SM yield, and it achieved the land equivalent ratio of 1.7. These results suggest that by maintaining the appropriate planting distances between maize and soybean we can improve the competitiveness and yield of intercrop species in relay-intercropping system.

    A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. I. Canopy cover dynamics
    Khan, Muhammad Sohail ; Struik, Paul C. ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Yin, Xinyou - \ 2019
    Field Crops Research 242 (2019). - ISSN 0378-4290
    Genotype-by-environment interaction - Haulm growth - Heritability - Maturity type - QTL mapping

    We designed a model to quantify the canopy cover dynamics in potato (Solanum tuberosum L.). It describes the dynamics during the build-up phase, maximum cover phase, and decline phase of canopy development through five parameters defining timing of three phases and maximum canopy cover (vmax). These five parameters were estimated for 100 individuals of an F1 population, their parents, and five standard cultivars, using data from six field experiments, and used to estimate secondary traits, related to duration and area under the canopy cover curve for the three phases. The duration of the canopy build-up phase (DP1) was rather conserved, but the duration of maximum canopy cover (DP2) and the decline phase (DP3) varied greatly, with late maturing genotypes having longer DP2 and DP3 and thus a higher area under the canopy cover curve (Asum). High genetic variability coupled with high heritability was recorded for end of canopy senescence (te), DP2 and Asum. Strong positive phenotypic and genetic correlations were observed between DP2 and te, vmax or Asum indicating that genotypes with longer DP2 could be indirectly obtained by selecting for these traits. Several quantitative trait loci (QTLs) were detected for model traits explaining the variance by up to 74%. Clustering of many QTLs were found on position 18.2 cM on paternal linkage group V with major additive effects. Many additional QTLs with minor effects were mostly associated with maternal linkage groups. Our model approach could be used to exploit available genetic variability in canopy cover dynamics of potato.

    Analyzing the coexistence of conflict and cooperation in a regional delta management system: Tidal River Management (TRM) in the Bangladesh delta
    Mutahara, Mahmuda ; Warner, Jeroen ; Shah Alam Khan, M. - \ 2019
    Environmental Policy and Governance 29 (2019)5. - ISSN 1756-932X - p. 326 - 343.
    coexistence - conflict - cooperation - intensity - multistakeholder processes - participation - water governance

    This article analyzes the history and dynamics of conflict and cooperation in a local and regional delta management system focusing on tidal river management (TRM). TRM was formally implemented through a participatory approach since early 2000 to address waterlogging problems in the southwest delta of Bangladesh. There have been, and still are, serious difficulties in achieving the full potential of TRM because multistakeholder processes (MSPs) are not effectively sustained. One major cause of ineffective MSPs is incompetent dealing with conflict and cooperation among stakeholders. Our research was a participatory assessment of water management events focusing on the causes, intensity, and trend of conflict and cooperation in TRM practices over the last 30 years. The results show that the history of TRM appeared more conflictive than cooperative, and also the cooperations between major stakeholders were rarely sustained in TRM practices. To that effect, we applied an adapted “Transboundary Water Interaction Nexus (TWINs)” model to this local water management context, which explores the interrelatedness of conflict and cooperation for learning to deal with MSPs in local delta water management. The research findings should be helpful for improving participation policy in water management in Bangladesh and also facilitate MSPs in delta water governance elsewhere.

    Occurrence and characterization of methicillin resistant Staphylococcus aureus in processed raw foods and ready-to-eat foods in an urban setting of a developing country
    Islam, Mohammad Aminul ; Parveen, Sahana ; Rahman, Mahdia ; Huq, Mohsina ; Nabi, Ashikun ; Khan, Zahed Uddin Mahmood ; Ahmed, Niyaz ; Wagenaar, Jaap A. - \ 2019
    Frontiers in Microbiology 10 (2019)MAR. - ISSN 1664-302X
    Methicillin resistant S. aureus - MLST - Raw meat - Ready-to-eat foods - Spa typing

    Infections by methicillin-resistant Staphylococcus aureus (MRSA) are gradually increasing in the community. In this study, we investigated a total of 162 food samples including 112 ready-to-eat (RTE) foods and 40 processed raw meat and fish samples collected from retail vendors in Dhaka, Bangladesh and determined the occurrence of toxigenic S. aureus and MRSA. Around 22% of samples were positive for S. aureus, RTE foods being more positive (23%) than the processed raw meat/fish samples (18%). Among 35 S. aureus isolates, 74% were resistant to erythromycin, 49% to ciprofloxacin and around 30% to oxacillin and cefoxitin. Around 37% of isolates were resistant to ≥3 classes of antibiotics and 26% of isolates (n = 9) were identified as MRSA. Majority of the isolates were positive for enterotoxin genes (74%), followed by pvl gene (71%), toxic shock syndrome toxin (tsst) gene (17%) and exfoliative toxin genes (11%). Multi locus sequence typing (MLST) of 9 MRSA isolates identified four different types such as ST80 (n = 3), ST6 (n = 2), ST239 (n = 2) and ST361 (n = 2). spa typing of MRSA isolates revealed seven different types including t1198 (n = 2), t315 (n = 2), t037 (n = 1), t275 (n = 1), t304 (n = 1), t8731 (n = 1) and t10546 (n = 1). To our knowledge, this is the first report entailing baseline data on the occurrence of MRSA in RTE foods in Dhaka highlighting a potential public health risk to street food consumers.

    sPlot – A new tool for global vegetation analyses
    Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
    Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
    biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

    Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

    Rethinking sediments, tidal rivers and delta livelihoods : Tidal river management as a strategic innovation in Bangladesh
    Seijger, Chris ; Datta, Dilip Kumar ; Douven, Wim ; Halsema, Gerardo van; Khan, Malik Fida - \ 2019
    Water Policy 21 (2019)1. - ISSN 1366-7017 - p. 108 - 126.
    Delta management - Grassroots - Innovation - Planning - Silt - Strategic thinking - Transition

    Many urbanised deltas face development challenges due to growing economies, populations and climate change. Changes in land–water strategies are often required, as ‘business-as-usual’ solutions are no longer sufficient. The aim of this paper was to study tidal river management (TRM) as a strategic innovation, and trace how it is appreciated by people and used in master plans to address congested rivers and waterlogging in Bangladesh. In this context, a strategic innovation can be categorised as having four features: (i) it is a fundamental reconceptualisation of business as usual strategies; (ii) it is rule breaking and reshapes markets; (iii) it offers value improvement for livelihoods; (iv) it is sustainable. The case study analysis was built from 17 interviews, a focus group discussion and numerous documents. The case analysis revealed that tidal river management is very different (local, natural, complex) from mainstream engineering strategies for tidal rivers and polder systems, and is strongly supported by local people for its potential livelihood improvement. The paper concludes that tidal river management has strategic potential, though is hardly recognised in master plans. To advance practice, reconceptualisations are needed that focus on the diverse benefits of TRM, such as restored tidal rivers, flora and fauna. Further research could elaborate livelihood models that thrive on these benefits, and evaluate their costs and benefits accordingly.

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