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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Embryogenesis efficiency and genetic stability of Dianthus caryophyllus embryos in response to different light spectra and plant growth regulators
Aalifar, Mostafa ; Arab, Mostafa ; Aliniaeifard, Sasan ; Dianati, Shirin ; Zare Mehrjerdi, Mahboobeh ; Limpens, Erik ; Serek, Margrethe - \ 2019
Plant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants (2019). - ISSN 0167-6857 - 14 p.
Carnation - Embryogenesis - ISSR marker - Light spectrum

Carnation is an important cut flower with industrial and medicinal applications. To establish an efficient protocol without somaclonal variation for micropropagation of Dianthus caryophyllus, direct and indirect somatic embryogenesis (DSE and ISE) were investigated under six different light spectra (white, red, green, blue, red + blue and far red + red) and four combinations of different plant growth regulators (PGRs) never tested so far for carnation. The best results were achieved with 2,4-dichlorophenoxyacetic acid (2,4-D) + N-(2-chloro-4-pyridyl)-N′-phenylurea (4-CPPU) for ISE and picloram + 4-CPPU or naphthoxyacetic acid (NOA) + 6-benzylaminopurine (BAP) for DSE. The DSE method was faster (3 weeks compared to 8 weeks) and easier (no subculturing compared to two rounds of subculture with ISE methods) but the percentage of somatic embryos in the ISE method was higher compared to the DSE method. Our results showed that the highest DSE, formation of embryogenic callus, embryo maturation (generation of globular, heart and torpedo shapes) and ISE rate was observed in carnation explants exposed to blue light (450–495 nm). In contrast, green (495–570 nm), red (610–700) and far red (710–730 nm) lights caused negative effects on embryogenesis compared to white light controls (380–750 nm). For the first time, genetic stability of regenerated carnation plants was estimated using inter-simple sequence repeat (ISSR) markers. The amplified products showed 75 distinct and scorable bands, and regenerants [plants obtained by primary (PSE) and secondary SE (SSE)] were completely identical to the mother plant. Similarly, flow cytometric analysis confirmed that somatic embryo-derived plants had on average 1.53 pg nuclear DNA (2C), and all plants maintained their ploidy. In conclusion, obtained embryos under blue light were big in size and torpedo-shaped and their germination was highest compared to other light spectra. Moreover, blue light was effective for direct and indirect somatic embryogenesis in carnation without induction of somaclonal variation.

Structural Plasticity of Intrinsically Disordered LEA Proteins from Xerophyta schlechteri Provides Protection In Vitro and In Vivo
Silva Artur, Mariana A. ; Rienstra, Juriaan ; Dennis, Timothy J. ; Farrant, Jill M. ; Ligterink, Wilco ; Hilhorst, Henk - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
intrinsic disorder - late embryogenesis abundant proteins - plant desiccation tolerance - resurrection plants - Xerophyta

Late embryogenesis abundant (LEA) proteins are essential to the ability of resurrection plants and orthodox seeds to protect the subcellular milieu against irreversible damage associated with desiccation. In this work, we investigated the structure and function of six LEA proteins expressed during desiccation in the monocot resurrection species Xerophyta schlechteri (XsLEAs). In silico analyses suggested that XsLEAs are hydrophilic proteins with variable intrinsically disordered protein (IDP) properties. Circular dichroism (CD) analysis indicated that these proteins are mostly unstructured in water but acquire secondary structure in hydrophobic solution, suggesting that structural dynamics may play a role in their function in the subcellular environment. The protective property of XsLEAs was demonstrated by their ability to preserve the activity of the enzyme lactate dehydrogenase (LDH) against desiccation, heat and oxidative stress, as well as growth of Escherichia coli upon exposure to osmotic and salt stress. Subcellular localization analysis indicated that XsLEA recombinant proteins are differentially distributed in the cytoplasm, membranes and nucleus of Nicotiana benthamiana leaves. Interestingly, a LEA_1 family protein (XsLEA1-8), showing the highest disorder-to-order propensity and protective ability in vitro and in vivo, was also able to enhance salt and drought stress tolerance in Arabidopsis thaliana. Together, our results suggest that the structural plasticity of XsLEAs is essential for their protective activity to avoid damage of various subcellular components caused by water deficit stress. XsLEA1-8 constitutes a potential model protein for engineering structural stability in vitro and improvement of water-deficit stress tolerance in plants.

A European inter-laboratory trial to evaluate the performance of three serological methods for diagnosis of Mycoplasma bovis infection in cattle using latent class analysis
Andersson, Anna Maria ; Aspán, Anna ; Wisselink, Henk J. ; Smid, Bregtje ; Ridley, Anne ; Pelkonen, Sinikka ; Autio, Tiina ; Lauritsen, Klara Tølbøll ; Kensø, Jane ; Gaurivaud, Patrice ; Tardy, Florence - \ 2019
BMC Veterinary Research 15 (2019)1. - ISSN 1746-6148 - 1 p.
ELISA - Inter-laboratory trial - Latent class analysis - Mycoplasma bovis cattle - Western blot

BACKGROUND: Mycoplasma bovis (M. bovis) is an emerging bovine pathogen, leading to significant economic losses in the livestock industry worldwide. Infection can result in a variety of clinical signs, such as arthritis, pneumonia, mastitis and keratoconjunctivitis, none of which are M. bovis-specific. Laboratory diagnosis is therefore important. Serological tests to detect M. bovis antibodies is considered an effective indicator of infection in a herd and often used as a herd test. Combined with clinical judgement, it can also be used to implement control strategies and/or to estimate the disease prevalence within a country. However, due to lack of harmonisation of approaches to testing, and serological tests used by different laboratories, comparisons of prevalence data between countries is often difficult. A network of researchers from six European countries designed and participated in an inter-laboratory trial, with the aim of evaluating the sensitivity (Se) and specificity (Sp) of two commercially available ELISA tests (ID Screen® ELISA (IDvet) and BIO K302 ELISA (BIO-X Diagnostics)) for diagnosis of M. bovis infection. Each laboratory received a blinded panel of bovine sera and tested independently, according to manufacturer's instructions. Western blot analyses (WB) performed by one of the participating laboratories was used as a third diagnostic test in the statistical evaluation of Se and Sp values using latent class analysis. RESULTS: The Se of WB, the ID Screen® ELISA and the BIO K302 ELISA were determined to be 91.8, 93.5 and 49.1% respectively, and corresponding Sp of the three tests were 99.6, 98.6 and 89.6%, respectively. CONCLUSIONS: The present study is, to our knowledge, the first to present an inter-laboratory comparison of the BIO K302 ELISA and the ID Screen® ELISA. Based on our results, the ID Screen® ELISA showed high consistency with WB and performed with higher precision and accuracy than the BIO K302 ELISA.

Fermented cereal-based Munkoyo beverage: Processing practices, microbial diversity and aroma compounds
Phiri, Sydney ; Schoustra, Sijmen E. ; Heuvel, Joost van den; Smid, Eddy J. ; Shindano, John ; Linnemann, Anita - \ 2019
PLoS ONE 14 (2019)10. - ISSN 1932-6203

Fermented cereal-based foods play a crucial role in attaining food and nutrition security for resource-poor populations in sub-Saharan Africa. These products are widely produced by spontaneous fermentation using of cereal grains as raw material. They have a unique taste and flavour, are rich sources of energy and their non-alcoholic nature makes them ideal for consumption by the entire population, including children. Lactic acid bacteria dominate the fermentation process and lead to a low pH of around 4, which suppresses the growth of pathogenic bacteria, thereby increasing the shelf-life and safety of the food. Knowledge about processing practices, consumption patterns and bacterial communities is essential to regulate processing and design appropriate mixes of micro-organisms to produce starter cultures for commercial production of standard-quality fermented foods that meet desired quality characteristics. In four regions of Zambia, we surveyed processing practices and consumption patterns of a spontaneously fermented cereal-based beverage called Munkoyo, commonly produced in Zambia and the Democratic Republic of Congo. Variations in processing practices exist in cooking time of the unfermented maize porridge and time allowed for fermentation. Consumption is mainly at household level and the product is considered as an energy drink. Characterisation of the bacterial communities of over 90 samples with 16S amplicon sequencing on DNA extracted from the entire bacterial community revealed six dominant families, namely Streptococcaceae, Leuconostocaceae, Enterobacteriaceae, Lactabacillales, Bacillaceae and Aeromonadaceae, and a Shannon index of up to 1.18 with an effective number of 3.44 bacterial species. Bacterial communities that underlie the fermentation in Munkoyo differ in their composition for the different regions using common processing steps, suggesting that different combinations of bacteria can be used to achieve successful Munkoyo fermentation. Analysis of aroma profiles in 15 different samples from two different Provinces showed that aldehydes, esters, organic acids, alkanes, alkenes and alcohols dominated.

Influência do ambiente de armazenamento na qualidade fisiológica de sementes de milheto (Pennisetum glaucum (L.) R. Br
Silva, Girlânio Holanda da; Toledo, Mariana Zampar ; Teixeira, Renake Nogueira ; Rossi, Rubiana Falopa ; Nakagawa, João - \ 2019
Journal of seed science 41 (2019)3. - ISSN 2317-1537 - p. 286 - 292.
Conservation - Germination - Physiological quality

Millet is a species of the grass family used in cattle pastures, for hay, for silage, and in soil cover in no-tillage systems. However, studies on seed production and post-harvest techniques for this species have not been sufficiently developed, considering the demand for and potential of this crop. The objective of this study was to monitor the physiological quality of millet seeds stored in porous packaging. Millet seeds were stored under four ambient conditions (natural laboratory environment, dry chamber, refrigerator, and freezer). Physiological quality was evaluated by germination and vigor tests before and during storage each year, up to six years for the dry chamber and natural laboratory environment, and up to 12 years for the refrigerator and freezer. Analysis of variance was conducted on the data, which were in 4 × 6 and 2 × 12 (environment and storage period) factorial arrangements. The means of the environments were compared by the Tukey test (p ≤ 0.05) and the storage periods by regression analysis. The germination capacity of millet seeds is best conserved in a refrigerator and freezer, and they remain viable for up to twelve years of storage under these conditions.

Dietary fibre enrichment of supplemental feed modulates the development of the intestinal tract in suckling piglets
Hees, H.M.J. Van; Davids, M. ; Maes, D. ; Millet, S. ; Possemiers, S. ; Hartog, L.A. Den; Kempen, T.A.T.G. Van; Janssens, G.P.J. - \ 2019
Journal of Animal Science and Biotechnology 10 (2019)1. - ISSN 1674-9782
Dietary fibre - Gut maturation - Gut microbiota - Suckling piglets

Background: Commercial pre-weaning diets are formulated to be highly digestible and nutrient-dense and contain low levels of dietary fibre. In contrast, pigs in a natural setting are manipulating fibre-rich plant material from a young age. Moreover, dietary fibre affects gastrointestinal tract (GIT) development and health in older pigs. We hypothesised that supplemental diets that contain vegetal fibres are accelerating GIT development in suckling piglets in terms of size and functionality. From d 2 of life, sow-suckled piglets had access to a low fibre diet (CON), a diet with a fermentable long-chain arabinoxylan (lc-AXOS), a diet with a largely non-fermentable purified cellulose (CELL), or a diet containing both fibres. During the initial 2 weeks, the control diet was a high-density milk replacer, followed by a dry and highly digestible creep meal. Upon weaning at 25 d, 15 piglets from each treatment group, identified as eaters and originating from six or seven litters, were sacrificed for post-mortem examination of GIT morphology, small intestinal permeability and metabolic profile of the digesta. The microbiota composition of the mid-colon was evaluated in a sub-set of ten piglets. Results: No major statistical interactions between the fibre sources were observed. Piglets consumed the fibre-containing milk supplements and creep diets well. Stomach size and small intestinal permeability was not affected. Large intestinal fill was increased with lc-AXOS only, while relative large intestinal weight was increased with both fibre sources (P < 0.050). Also, CELL decreased ileal pH and tended to increase ileal DM content compared to CON (P < 0.050). Moreover, the concentration of volatile fatty acids was increased in the caecum (P < 0.100) and mid-colon (P < 0.050) by addition of CELL. lc-AXOS only stimulated caecal propionate (P < 0.050). The microbiota composition showed a high individual variation and limited dietary impact. Nonetheless, CELL induced minor shifts in specific genera, with notable reductions of Escherichia-Shigella. Conclusions: Adding dietary fibres to the supplemental diet of suckling piglets altered large intestinal morphology but not small intestinal permeability. Moreover, dietary fibre showed effects on fermentation and modest changes of microbial populations in the hindgut, with more prominent effects from the low-fermentable cellulose.

Cultivation of Sponge-Associated Bacteria from Agelas sventres and Xestospongia muta Collected from Different Depths
Indraningrat, Anak Agung Gede ; Micheller, Sebastian ; Runderkamp, Mandy ; Sauerland, Ina ; Becking, Leontine E. ; Smidt, Hauke ; Sipkema, Detmer - \ 2019
Marine Drugs 17 (2019)10. - ISSN 1660-3397
Bacteria - Cultivation - Depth - Sponges

Sponge-associated bacteria have been mostly cultured from shallow water (≤30 m) sponges, whereas only few studies targeted specimens from below 30 m. This study assessed the cultivability of bacteria from two marine sponges Xestospongia muta and Agelas sventres collected from shallow (<30 m), upper mesophotic (30–60 m), and lower mesophotic (60–90 m) reefs. Sponge-associated bacteria were cultivated on six different media, and replicate plates were used to pick individual colonies or to recover the entire biomass. Prokaryotic community analysis was conducted using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 144 bacterial isolates were picked following a colony morphology coding scheme and subsequently identified by 16S rRNA gene sequence analysis. Sponge individuals at each depth-range harboured specific cultivable bacteria that were not retrieved from specimens collected at other depths. However, there were substantial differences in the number of colonies obtained for replicate sponges of the same species. In addition, source of inoculum and cultivation medium had more impact on the cultured prokaryotic community than sample collection depth. This suggests that the “plate count anomaly” is larger than differences in sponge-associated prokaryotic community composition related to depth.

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.

Disentangling ‘ecosystem services’ and ‘nature’s contributions to people’
Kadykalo, Andrew N. ; López-Rodriguez, María D. ; Ainscough, Jacob ; Droste, Nils ; Ryu, Hyeonju ; Ávila-Flores, Giovanni ; Clec’h, Solen Le; Muñoz, Marcia C. ; Nilsson, Lovisa ; Rana, Sakshi ; Sarkar, Priyanka ; Sevecke, Katharina J. ; Harmáčková, Zuzana V. - \ 2019
Ecosystems and People 15 (2019)1. - ISSN 2639-5908 - p. 269 - 287.
Ecosystem services - IPBES - nature’s benefits to people - nature’s contributions to people - NCP - Patricia Balvanera - people and nature - science–policy interface

People depend on functioning ecosystems, which provide benefits that support human existence and wellbeing. The relationship between people and nature has been experienced and conceptualized in multiple ways. Recently, ecosystem services (ES) concepts have permeated science, government policies, multi-national environmental agreements, and science–policy interfaces. In 2017, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) introduced a new and closely related concept–Nature’s Contributions to People (NCP). The introduction of NCP has sparked some lively discussion and confusion about the distinguishing characteristics between ES and NCP. In order to clarify their conceptual relation, we identify eleven specific claims about novel elements from the latest NCP literature and analyze how far ES research has already contributed to these corresponding conceptual claims in the existing ES literature. We find a mixed-picture, where on six specific conceptual claims (culture, social sciences and humanities, indigenous and local knowledge, negative contributions of nature, generalizing perspective, non-instrumental values and valuation) NCP does not differ greatly from past ES research, but we also find five conceptual claims (diverse worldviews, context-specific perspective, relational values, fuzzy and fluid reporting categories and groups, inclusive language and framing) where NCP provides novel conceptualizations of people and nature relations.

Variation in performance and resistance to parasitism of Plutella xylostella populations
Gols, Rieta ; Desurmont, Gaylord A. ; Harvey, Jeffrey A. - \ 2019
Insects 10 (2019)9. - ISSN 2075-4450
Diamondback moth - Genetic variation - Host immunity - Host-plant adaptation - Insect-herbivore interactions - Parasitoid - Plant resistance

Two major ecological factors determine the fitness of an insect herbivore: the ability to overcome plant resistance strategies (bottom-up effects) and the ability to avoid or resist attack by natural enemies such as predators and parasitoids (top-down effects). In response to differences in selection pressure, variation may exist in host-plant adaptation and immunity against parasitism among populations of an insect herbivore. We investigated the variation in larval performance of six different Plutella xylostella populations originating from four continents when feeding on a native Dutch plant species, Brassica rapa. One of the used populations has successfully switched its host plant, and is now adapted to pea. In addition, we determined the resistance to attack by the endoparasitoid Diadegma semiclausum originating from the Netherlands (where it is also native) and measured parasitoid performance as a proxy for host resistance against parasitism. Pupal mortality, immature development times, and adult biomass of P. xylostella differed significantly across populations when feeding on the same host plant species. In addition, parasitism success differed in terms of parasitoid adult emergence and their biomass, but not their development times. Variation among natural populations of insects should be considered more when studying interactions between plants and insects up the food chain.

A protocol to develop Shared Socio-economic Pathways for European agriculture
Mitter, Hermine ; Techen, Anja K. ; Sinabell, Franz ; Helming, Katharina ; Kok, Kasper ; Priess, Jörg A. ; Schmid, Erwin ; Bodirsky, Benjamin L. ; Holman, Ian ; Lehtonen, Heikki ; Leip, Adrian ; Mouël, Chantal Le; Mathijs, Erik ; Mehdi, Bano ; Michetti, Melania ; Mittenzwei, Klaus ; Mora, Olivier ; Øygarden, Lillian ; Reidsma, Pytrik ; Schaldach, Rüdiger ; Schönhart, Martin - \ 2019
Journal of Environmental Management 252 (2019). - ISSN 0301-4797
Climate change - Consistent storylines - Eur-Agri-SSP - Integrated assessment - Narrative - Social environmental system

Moving towards a more sustainable future requires concerted actions, particularly in the context of global climate change. Integrated assessments of agricultural systems (IAAS) are considered valuable tools to provide sound information for policy and decision-making. IAAS use storylines to define socio-economic and environmental framework assumptions. While a set of qualitative global storylines, known as the Shared Socio-economic Pathways (SSPs), is available to inform integrated assessments at large scales, their spatial resolution and scope is insufficient for regional studies in agriculture. We present a protocol to operationalize the development of Shared Socio-economic Pathways for European agriculture – Eur-Agri-SSPs – to support IAAS. The proposed design of the storyline development process is based on six quality criteria: plausibility, vertical and horizontal consistency, salience, legitimacy, richness and creativity. Trade-offs between these criteria may occur. The process is science-driven and iterative to enhance plausibility and horizontal consistency. A nested approach is suggested to link storylines across scales while maintaining vertical consistency. Plausibility, legitimacy, salience, richness and creativity shall be stimulated in a participatory and interdisciplinary storyline development process. The quality criteria and process design requirements are combined in the protocol to increase conceptual and methodological transparency. The protocol specifies nine working steps. For each step, suitable methods are proposed and the intended level and format of stakeholder engagement are discussed. A key methodological challenge is to link global SSPs with regional perspectives provided by the stakeholders, while maintaining vertical consistency and stakeholder buy-in. We conclude that the protocol facilitates systematic development and evaluation of storylines, which can be transferred to other regions, sectors and scales and supports inter-comparisons of IAAS.

Distinct genomic signals of lifespan and life history evolution in response to postponed reproduction and larval diet in Drosophila
Hoedjes, Katja M. ; Heuvel, Joost Van Den; Kapun, Martin ; Keller, Laurent ; Flatt, Thomas ; Zwaan, Bas J. - \ 2019
Evolution Letters (2019). - ISSN 2056-3744
Reproduction and diet are two major factors controlling the physiology of aging and life history, but how they interact to affect the evolution of longevity is unknown. Moreover, although studies of large‐effect mutants suggest an important role of nutrient sensing pathways in regulating aging, the genetic basis of evolutionary changes in lifespan remains poorly understood. To address these questions, we analyzed the genomes of experimentally evolved Drosophila melanogaster populations subjected to a factorial combination of two selection regimes: reproductive age (early versus postponed), and diet during the larval stage (“low,” “control,” “high”), resulting in six treatment combinations with four replicate populations each. Selection on reproductive age consistently affected lifespan, with flies from the postponed reproduction regime having evolved a longer lifespan. In contrast, larval diet affected lifespan only in early‐reproducing populations: flies adapted to the “low” diet lived longer than those adapted to control diet. Here, we find genomic evidence for strong independent evolutionary responses to either selection regime, as well as loci that diverged in response to both regimes, thus representing genomic interactions between the two. Overall, we find that the genomic basis of longevity is largely independent of dietary adaptation. Differentiated loci were not enriched for “canonical” longevity genes, suggesting that naturally occurring genic targets of selection for longevity differ qualitatively from variants found in mutant screens. Comparing our candidate loci to those from other “evolve and resequence” studies of longevity demonstrated significant overlap among independent experiments. This suggests that the evolution of longevity, despite its presumed complex and polygenic nature, might be to some extent convergent and predictable.
Microarray experiment comparing gene expression in the bar-1 mutant EW15 with wild-type strain N2 in Caenorhabditis elegans
Sterken, M.G. - \ 2019
Wageningen University & Research
E-MTAB-8128 - Caenorhabditis elegans
The Wnt-pathway is a key-signalling pathway in metazoans. The beta-catenins, which include bar-1, have a function in gene expression regulation in Wnt-signalling. In this study, the effect of a loss-of-function mutation (bar-1(ga80) in the strain EW15) on gene-expression was tested. To this end age-synchronized populations of both N2 (wild-type) and EW15 were grown for 48 hours at 20 degrees Celsius, after which populations were collected and total RNA was isolated. For each genotype six replicates were collected in three batches of two replicates.
Relative preference for wooden nests affects nesting behaviour of broiler breeders
Oever, Anna C.M. van den; Rodenburg, T.B. ; Bolhuis, J.E. ; Ven, Lotte J.F. van de; Hasan, Md Kamrul ; Aerle, Stephanie M.W. van; Kemp, Bas - \ 2019
Applied Animal Behaviour Science (2019). - ISSN 0168-1591
Behaviour - Broiler breeder - Nest design - Preference test - Welfare

Optimising nest design for broiler breeders has benefits for both the animals and the producers. The welfare of the hens will increase by providing preferred housing, while also reducing eggs laid outside the nests. These floor eggs cause economic losses by compromised automatic egg collection and reduced saleability and hatchability. Attractiveness of nests can involve factors such as seclusion, material and microclimate. In this study, four nest box designs were offered in a relative preference test: a plastic control nest, a plastic nest with a partition to divide the nest in two areas, a plastic nest with a ventilator underneath to create air flow inside the nest and a wooden nest. Six groups of 100 hens and 9 roosters had access to these four nests in a randomised location during the ages of 20 to 34 weeks. Nest and floor eggs were collected five days a week. Camera images from inside the nests made during the ages of 24–25 weeks and 26–27 weeks were analysed for behaviour. This included general activity, nest inspections, nest visits and social interactions. At 32 weeks of age the wooden nests were closed, and the subsequent response of the hens was monitored in terms of number of eggs. We found a clear preference in number of eggs for the wooden nest (69.3 ± 1.0%) compared to the control nest (15.1 ± 0.8%), partition nest (10.2 ± 0.5%) and the ventilator nest (5.4 ± 0.4%; p<0.0001 for difference between all nest designs). The preference for the wooden nest was also reflected in an increased time spent sitting, together with fewer nest inspections and visits per egg laid in the wooden nest. The preference for the wooden nest led to crowding, which caused an increased amount of piling, nest displacement, aggression and head shaking. The fact that the hens were willing to accept the crowded circumstances in these nests, underlines the strength of this preference. After the wooden nests were closed, the hens chose a new nest based on a combination of nest design and location. The control nest was still preferred over the other two plastic designs, although the neighbouring nests were overall preferred to the non-neighbouring nests. This study shows how the material used for nests is an important factor in suitability and should therefore be taken into account when designing nests.

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut
Hynönen, Ulla ; Zoetendal, Erwin G. ; Virtala, Anna Maija K. ; Shetty, Sudarshan ; Hasan, Shah ; Jakava-Viljanen, Miia ; Vos, Willem M. de; Palva, Airi - \ 2019
Anaerobe (2019). - ISSN 1075-9964
16S rRNA - IBS - Intestinal microbiota - Typing - Uncultured

In our previous studies on irritable bowel syndrome (IBS) –associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) –sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.

Resource use efficiency of indoor lettuce (Lactuca sativa L.) cultivation as affected by red:blue ratio provided by LED lighting
Pennisi, Giuseppina ; Orsini, Francesco ; Blasioli, Sonia ; Cellini, Antonio ; Crepaldi, Andrea ; Braschi, Ilaria ; Spinelli, Francesco ; Nicola, Silvana ; Fernandez, Juan A. ; Stanghellini, Cecilia ; Gianquinto, Giorgio ; Marcelis, Leo F.M. - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 11 p.

LED lighting in indoor farming systems allows to modulate the spectrum to fit plant needs. Red (R) and blue (B) lights are often used, being highly active for photosynthesis. The effect of R and B spectral components on lettuce plant physiology and biochemistry and resource use efficiency were studied. Five red:blue (RB) ratios (0.5-1-2-3-4) supplied by LED and a fluorescent control (RB = 1) were tested in six experiments in controlled conditions (PPFD = 215 μmol m-2 s-1, daylength 16 h). LED lighting increased yield (1.6 folds) and energy use efficiency (2.8 folds) as compared with fluorescent lamps. Adoption of RB = 3 maximised yield (by 2 folds as compared with RB = 0.5), also increasing leaf chlorophyll and flavonoids concentrations and the uptake of nitrogen, phosphorus, potassium and magnesium. As the red portion of the spectrum increased, photosystem II quantum efficiency decreased but transpiration decreased more rapidly, resulting in increased water use efficiency up to RB = 3 (75 g FW L-1 H2O). The transpiration decrease was accompanied by lower stomatal conductance, which was associated to lower stomatal density, despite an increased stomatal size. Both energy and land surface use efficiency were highest at RB ≥ 3. We hereby suggest a RB ratio of 3 for sustainable indoor lettuce cultivation.

Using Unmanned Aerial Systems (UAS) and Object-Based Image Analysis (OBIA) for Measuring Plant-Soil Feedback Effects on Crop Productivity
Nuijten, Rik J.G. ; Kooistra, Lammert ; Deyn, Gerlinde B. De - \ 2019
Drones 3 (2019)3. - ISSN 2504-446X
Unmanned aerial system (UAS) acquired high-resolution optical imagery and object-based image analysis (OBIA) techniques have the potential to provide spatial crop productivity information. In general, plant-soil feedback (PSF) field studies are time-consuming and laborious which constrain the scale at which these studies can be performed. Development of non-destructive methodologies is needed to enable research under actual field conditions and at realistic spatial and temporal scales. In this study, the influence of six winter cover crop (WCC) treatments (monocultures Raphanus sativus, Lolium perenne, Trifolium repens, Vicia sativa and two species mixtures) on the productivity of succeeding endive (Cichorium endivia) summer crop was investigated by estimating crop volume. A three-dimensional surface and terrain model were photogrammetrically reconstructed from UAS imagery, acquired on 1 July 2015 in Wageningen, the Netherlands. Multi-resolution image segmentation (MIRS) and template matching algorithms were used in an integrated workflow to detect individual crops (accuracy = 99.8%) and delineate C. endivia crop covered area (accuracy = 85.4%). Mean crop area (R = 0.61) and crop volume (R = 0.71) estimates had strong positive correlations with in situ measured dry biomass. Productivity differences resulting from the WCC treatments were greater for estimated crop volume in comparison to in situ biomass, the legacy of Raphanus was most beneficial for estimated crop volume. The perennial ryegrass L. perenne treatment resulted in a significantly lower production of C. endivia. The developed workflow has potential for PSF studies as well as precision farming due to its flexibility and scalability. Our findings provide insight into the potential of UAS for determining crop productivity on a large scale.
Transnational corporations and the challenge of biosphere stewardship
Folke, Carl ; Österblom, Henrik ; Jouffray, Jean Baptiste ; Lambin, Eric F. ; Adger, W.N. ; Scheffer, Marten ; Crona, Beatrice I. ; Nyström, Magnus ; Levin, Simon A. ; Carpenter, Stephen R. ; Anderies, John M. ; Chapin, Stuart ; Crépin, Anne Sophie ; Dauriach, Alice ; Galaz, Victor ; Gordon, Line J. ; Kautsky, Nils ; Walker, Brian H. ; Watson, James R. ; Wilen, James ; Zeeuw, Aart de - \ 2019
Nature Ecology & Evolution 3 (2019)10. - ISSN 2397-334X - p. 1396 - 1403.

Sustainability within planetary boundaries requires concerted action by individuals, governments, civil society and private actors. For the private sector, there is concern that the power exercised by transnational corporations generates, and is even central to, global environmental change. Here, we ask under which conditions transnational corporations could either hinder or promote a global shift towards sustainability. We show that a handful of transnational corporations have become a major force shaping the global intertwined system of people and planet. Transnational corporations in agriculture, forestry, seafood, cement, minerals and fossil energy cause environmental impacts and possess the ability to influence critical functions of the biosphere. We review evidence of current practices and identify six observed features of change towards 'corporate biosphere stewardship', with significant potential for upscaling. Actions by transnational corporations, if combined with effective public policies and improved governmental regulations, could substantially accelerate sustainability efforts.

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.

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