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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Exploring in vitro gastric digestion of whey protein by time-domain nuclear magnetic resonance and magnetic resonance imaging
Deng, Ruoxuan ; Janssen, Anja E.M. ; Vergeldt, Frank J. ; As, Henk Van; Graaf, Cees de; Mars, Monica ; Smeets, Paul A.M. - \ 2020
Food Hydrocolloids 99 (2020). - ISSN 0268-005X
Gastric digestion - Gel - In vitro - MRI - Time-domain NMR - Whey protein

Gastric digestion is crucial for protein breakdown. Although it has been widely studied with in vitro models, verification in vivo remains a big challenge. Magnetic resonance imaging (MRI) has the potential to bridge this gap. Our objective was to use the transverse relaxation time (T2) and rate (R2 = T2 −1) to monitor hydrolysis of protein-rich food during in vitro gastric digestion. Whey protein solution and heat-induced hydrogels were digested by means of simulated gastric fluid (SGF). Free amino groups (–NH2 groups) and protein concentration in the supernatant were measured. T2 and R2 of the digestion mixture were determined by time-domain nuclear magnetic resonance (TD-NMR) and MRI. Subsequently, relative amplitudes (TD-NMR) for different T2 values and T2 distribution (MRI) were determined. For the solution, protein concentration and T2 did not change during digestion. For the gels, water in supernatant and gel phase could be discriminated on the basis of their T2 values. During digestion, R2 of supernatant correlated positively with protein (–NH2 groups) concentration in SGF. Also, the decrease in relative amplitude of gel fraction correlated linearly with the increase of supernatant protein concentration. MRI T2-mapping showed similar associations between R2 of supernatant and protein (–NH2 groups) concentration. In conclusion, T2-measurements by TD-NMR and MRI can be used to monitor in vitro gastric digestion of whey protein gels; TD-NMR measurements contributed to interpreting the MRI data. Thus, MRI has high potential for monitoring in vivo gastric digestion and this should be further pursued.

Do diverse landscapes provide for effective natural pest control in subtropical rice?
Zou, Yi ; Kraker, Joop De; Bianchi, Felix J.J.A. ; Xiao, Haijun ; Huang, Jikun ; Deng, Xiangzheng ; Hou, Lingling ; Werf, Wopke Van Der - \ 2020
Journal of Applied Ecology 57 (2020)1. - ISSN 0021-8901 - p. 170 - 180.
While the biocontrol potential of natural enemies is well established, it is largely unknown how landscape‐mediated effects on pest and natural enemy communities impact the cascade of biocontrol potential, crop injury, yield and profit, taking into account crop management and surrounding landscape composition.We compared natural biocontrol with chemical control according to local farmers’ practice, across the ‘full cascade’ from natural enemy and pest abundance to crop injury, yield loss, yield and economic performance. This two‐year study was conducted in 20 rice fields embedded in a gradient of landscapes from crop‐dominated to semi‐natural habitat‐dominated, in subtropical China, the world's largest rice producing region.Natural enemies suppressed brown planthopper population growth in unsprayed plots, irrespective of landscape composition. However, crop injury was lower in pesticide treated plots than in unsprayed plots, and yields in sprayed plots were 20% higher than in unsprayed plots. Nevertheless, pesticide applications were only profitable in less than half of the cases when only costs for pesticides were considered, and in less than one third of the cases when costs for pesticides and labour were considered.Synthesis and applications. Our findings question the cost‐effectiveness of current chemical‐based pest management in farming, and highlight opportunities for more ecologically based pest management strategies based on the widespread activity of natural enemies. Pest damage and biocontrol, however, are largely independent from the landscape context, which might be due to the small‐scale character of Chinese rice landscapes. To maintain high levels of biocontrol, conserving this small‐scale character appears more important than increasing the proportion of semi‐natural habitat
Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)
Linsmith, Gareth ; Rombauts, Stephane ; Montanari, Sara ; Deng, Cecilia H. ; Celton, Jean Marc ; Guérif, Philippe ; Liu, Chang ; Lohaus, Rolf ; Zurn, Jason D. ; Cestaro, Alessandro ; Bassil, Nahla V. ; Bakker, Linda V. ; Schijlen, Elio ; Gardiner, Susan E. ; Lespinasse, Yves ; Durel, Charles Eric ; Velasco, Riccardo ; Neale, David B. ; Chagné, David ; Peer, Yves Van de; Troggio, Michela ; Bianco, Luca - \ 2019
GigaScience 8 (2019)12. - ISSN 2047-217X
chromosome-scale assembly - Hi-C - Pac-Bio sequencing - Pyrus communis L

BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.

Land tenure reform and grassland degradation in Inner Mongolia, China
Liu, Min ; Dries, Liesbeth ; Heijman, Wim ; Zhu, Xueqin ; Deng, Xiangzheng ; Huang, Jikun - \ 2019
China Economic Review 55 (2019). - ISSN 1043-951X - p. 181 - 198.
China - Fixed effects model - Grassland degradation - Land tenure reform - Privatisation

Since the start of the land tenure reform in the pastoral areas of China in the 1980s, grassland use rights have increasingly been assigned to individual households. However, this period has also been accompanied by extensive grassland degradation in China, which has raised the question of whether a tragedy of privatisation has occurred. This paper investigates the impact of land tenure reform on the changes in grassland condition, using data from 60 counties in Inner Mongolia between 1985 and 2008. A fixed effects model is employed to control for time-invariant factors. Two alternative model specifications in terms of land tenure reform and time-variant factors are conducted to verify the robustness of the estimation results. The results show that land tenure reform did not affect the grassland condition significantly, and the major drivers of grassland degradation include the land use change and the increase in market demand (meat prices). Thereby, we provide empirical evidence that the privatisation of grasslands did not cause grassland degradation in Inner Mongolia, China.

Application of microfluidics in the production and analysis of food foams
Deng, Boxin ; Ruiter, Jolet De; Schroën, Karin - \ 2019
Foods — Open Access Food Science Journal 8 (2019)10. - ISSN 2304-8158
Coalescence - Dynamic surface tension - Emulsions - Foams - Microfluidics - Monodispersity - Up-scaling

Emulsifiers play a key role in the stabilization of foam bubbles. In food foams, biopolymers such as proteins are contributing to long-term stability through several effects such as increasing bulk viscosity and the formation of viscoelastic interfaces. Recent studies have identified promising new stabilizers for (food) foams and emulsions, for instance biological particles derived from water-soluble or water-insoluble proteins, (modified) starch as well as chitin. Microfluidic platforms could provide a valuable tool to study foam formation on the single-bubble level, yielding mechanistic insights into the formation and stabilization (as well as destabilization) of foams stabilized by these new stabilizers. Yet, the recent developments in microfluidic technology have mainly focused on emulsions rather than foams. Microfluidic devices have been up-scaled (to some extent) for large-scale emulsion production, and also designed as investigative tools to monitor interfaces at the (sub)millisecond time scale. In this review, we summarize the current state of the art in droplet microfluidics (and, where available, bubble microfluidics), and provide a perspective on the applications for (food) foams. Microfluidic investigations into foam formation and stability are expected to aid in optimization of stabilizer selection and production conditions for food foams, as well as provide a platform for (large-scale) production of monodisperse foams.

Mito-docking: A Novel In Vivo Method to Detect Protein–Protein Interactions
Shao, Wei ; He, Lihong ; Deng, Fei ; Wang, Hualin ; Vlak, Just M. ; Hu, Zhihong ; Wang, Manli - \ 2019
Small Methods 3 (2019)10. - ISSN 2366-9608
in vivo - method - Mito-docking - nuclear import - protein–protein interactions

Many methods have been developed to detect protein–protein interactions (PPIs) and explore cellular processes. However, effective methods for detecting complicated PPIs under physical conditions are still in demand. Here, a simple and efficient mitochondria-docking (Mito-docking) method for PPI detection in vivo is developed. The strategy is to anchor a “bait” protein to mitochondrial outer membrane (MOM), and then trap the “prey” protein onto MOM. In this way, interacting signals are enriched to allow easy detection. This method efficiently detects the well-known interaction between two G protein subunits (Gγ2 with Gβ1) and is successfully applied to investigate the recognition of importin α superfamily members for the classical nuclear localization signal (NLS) of simian virus 40 (SV40) large T antigen, which are highly dynamic and not easily visualized by conventional methods. As far as is known, this is the first time that the interaction between human importin α receptors with NLSs has been visualized. The results prove that Mito-docking can be used as a simple, straightforward, and intuitive method to study PPIs qualitatively and quantitatively in vivo.

Using poly(β-hydroxybutyrate-β-hydroxyvalerate) as carbon source in biofloc-systems : Nitrogen dynamics and shift of Oreochromis niloticus gut microbiota
Liu, Gang ; Deng, Yale ; Verdegem, Marc ; Ye, Zhangying ; Zhu, Songming - \ 2019
Science of the Total Environment 694 (2019). - ISSN 0048-9697
Biodegradable polymers (BDPs) - Biofloc system - Carbohydrate - Gut microbiota - Nitrogen dynamic

Inorganic‑nitrogen removal is essential for the sustainable operation of aquaculture industry and also influences the health of aquatic animals, which may be accomplished by utilizing biofloc technology. In this paper, we studied the use of three different carbon sources 1) longan seed powder (LP), 2) Poly(β-hydroxybutyrate-β-hydroxyvalerate) (PHBV) and 3) synthesized PHBV and LP (PHBVL) in biofloc systems for 90 days to investigate the nitrogen dynamics and gut microbiota of Nile tilapia (Oreochromis niloticus). The PHBVL and PHBV groups had higher total inorganic‑nitrogen removal efficiencies (70.99 ± 19.45% and 63.54 ± 19.44%) than the LP group (35.02 ± 11.21%), which had an accumulation of nitrate. Meanwhile, the biofloc in PHBVL and PHBV group generally had a higher amino acid composition, particularly for methionine and lysine, but was not reflected in the tilapia muscle. High-throughput sequencing indicated that the different carbohydrates shaped different bacterial community compositions in the fish gut after exposure in the three environments for 90-day. These differences, which resulted in different gut digestive enzyme activities (amylase, lipase and trypsin), and growth performance, which the food conversion ratio in the PHBVL group was lower than LP and PHBV group, the final body weight in PHBVL group was average 4.33% and 3.65% bigger than in LP and PHBV group. Network analysis revealed that the keystone taxa (90.33%) were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes, Verrucomicrobia and Bacteroidetes, which relative abundance varied in the fish gut in the three groups. The experiment verified the feasibility and advantage to use biodegradable polymers (BDPs) as carbohydrates for biofloc systems.

Do diverse landscapes provide for effective natural pest control in subtropical rice?
Zou, Y. ; Kraker, Joop de; Bianchi, F.J.J.A. ; Xiao, Haijun ; Huang, Jikun ; Deng, Xiangzheng ; Hou, Lingling ; Werf, W. van der - \ 2019
Wageningen University & Research
agroecosystem - biological pest control - China - natural enemy - pest - planthopper - yield
This datasets comprises data from 20 rice fields embedded in a gradient of landscapes from crop-dominated to semi-natural habitat-dominated, in the Jiangxi Province in China in 2014 and 2015. Each field was split into two plots: in one plot no pesticides were applied and in the other plot farmers applied pesticides according to their normal pest management practices. The dataset comprises information on the focal rice fields, the land use surrounding the focal rice fields, arthropod abundances and diversity, crop damage, an exclusion experiment to assess the potential of natural enemies to suppress pests, pest management practices and rice yield
Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations
Deng, Yale ; Ruan, Yunjie ; Ma, Bin ; Timmons, Michael B. ; Lu, Huifeng ; Xu, Xiangyang ; Zhao, Heping ; Yin, Xuwang - \ 2019
Environment International 132 (2019). - ISSN 0160-4120
Denitrification - Microbial aggregation - Multi-omics - Network - Niche difference

Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.

The Major Hurdle for Effective Baculovirus Transduction into Mammalian Cells Is Passing Early Endosomes
Hu, Liangbo ; Li, Yimeng ; Ning, Yun Jia ; Deng, Fei ; Vlak, Just M. ; Hu, Zhihong ; Wang, Hualin ; Wang, Manli - \ 2019
Journal of Virology 93 (2019)15. - ISSN 0022-538X
baculovirus - early endosome - entry - fusion - gene delivery - mammalian cells - transduction

Baculoviruses, although they infect insects in nature, can transduce a wide variety of mammalian cells and are therefore promising gene therapy vectors. However, baculovirus transduction into many mammalian cells is very inefficient, and the limiting stages and factors remain unknown. An important finding is that a short-duration trigger with low pH can significantly enhance virus transduction efficiency, but the mechanism is poorly understood. Herein, we performed a detailed comparative study on entry mechanisms of the prototypical baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) into insect and mammalian cells. The results showed that AcMNPV could be internalized into mammalian cells efficiently, but fusion in early endosomes (EEs) appeared to be the major obstacle. Measurement of endosomal pH suggested that virus fusion might be restricted under relatively high-pH conditions in mammalian cells. Interestingly, mutations of the major viral fusion protein GP64 that conferred decreased fusogenicity did not affect virus infection of insect cells, whereas virus transduction into mammalian cells was severely impaired, suggesting a more stringent dependence on GP64 fusogenicity for AcMNPV entry into mammalian cells than into insect cells. An increase in the fusogenicity of GP64 mutants resulting from low pH triggered the rescue of fusion-deficient recombinant virus transduction efficiency. Based on the above-described findings, the pH of EEs was specifically reduced with a Na+/K+-ATPase inhibitor, and the AcMNPV transduction of many mammalian cells indeed became highly efficient. This study not only revealed the roadblocks to mammalian cell entry of baculovirus but also provides a new strategy for improving baculovirus-based gene delivery and therapy.IMPORTANCE Baculoviruses can transduce a wide variety of mammalian cells but do so with low efficiency, which greatly limits their practical application as potential gene delivery vectors. So far, the understanding of baculovirus entry into mammalian cells is obscure, and the limiting stages and factors are unclear. In this study, by comparatively analyzing the mechanisms of baculovirus entry into mammalian and insect cells, virus fusion during the early stage of endocytosis was revealed as the major obstacle for efficient baculovirus transduction into mammalian cells. A higher fusogenicity of the major viral fusion protein GP64 was found to be required for virus entry into mammalian cells than for entry into insect cells. Interestingly, by decreasing the pH of early endosomes with a specific agent, virus transduction of a wide range of mammalian cells was greatly enhanced. This study uncovers the roadblocks to mammalian cell entry of baculoviruses and presents mechanisms to overcome the roadblocks.

A Medicago truncatula SWEET transporter implicated in arbuscule maintenance during arbuscular mycorrhizal symbiosis
An, Jianyong ; Zeng, Tian ; Ji, Chuanya ; Graaf, Sanne de; Zheng, Zijun ; Xiao, Ting Ting ; Deng, Xiuxin ; Xiao, Shunyuan ; Bisseling, Ton ; Limpens, Erik ; Pan, Zhiyong - \ 2019
New Phytologist 224 (2019)1. - ISSN 0028-646X - p. 396 - 408.
arbuscular mycorrhiza (AM) - glucose - Medicago truncatula - sugar export - SWEET - symbiosis

Plants form a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, which facilitates the acquisition of scarce minerals from the soil. In return, the host plants provide sugars and lipids to its fungal partner. However, the mechanism by which the AM fungi obtain sugars from the plant has remained elusive. In this study we investigated the role of potential SWEET family sugar exporters in AM symbiosis in Medicago truncatula. We show that M. truncatula SWEET1b transporter is strongly upregulated in arbuscule-containing cells compared to roots and localizes to the peri-arbuscular membrane, across which nutrient exchange takes place. Heterologous expression of MtSWEET1b in a yeast hexose transport mutant showed that it mainly transports glucose. Overexpression of MtSWEET1b in M. truncatula roots promoted the growth of intraradical mycelium during AM symbiosis. Surprisingly, two independent Mtsweet1b mutants, which are predicted to produce truncated protein variants impaired in glucose transport, exhibited no significant defects in AM symbiosis. However, arbuscule-specific overexpression of MtSWEET1bY57A/G58D, which are considered to act in a dominant-negative manner, resulted in enhanced collapse of arbuscules. Taken together, our results reveal a (redundant) role for MtSWEET1b in the transport of glucose across the peri-arbuscular membrane to maintain arbuscules for a healthy mutually beneficial symbiosis.

Differential Effects of Dry vs. Wet Heating of β-Lactoglobulin on Formation of sRAGE Binding Ligands and sIgE Epitope Recognition
Zenker, Hannah E. ; Ewaz, Arifa ; Deng, Ying ; Savelkoul, Huub F.J. ; Neerven, R.J. van; Jong, Nicolette W. De; Wichers, Harry J. ; Hettinga, Kasper A. ; Teodorowicz, Malgorzata - \ 2019
Nutrients 11 (2019)6. - ISSN 2072-6643
aggregation - allergenicity - CML - glycation - IgE binding - sRAGE - β-lactoglobulin

The effect of glycation and aggregation of thermally processed β-lactoglobulin (BLG) on binding to sRAGE and specific immunoglobulin E (sIgE) from cow milk allergic (CMA) patients were investigated. BLG was heated under dry conditions (water activity < 0.7) and wet conditions (in phosphate buffer at pH 7.4) at low temperature (<73 °C) and high temperatures (>90 °C) in the presence or absence of the milk sugar lactose. Nε-(carboxymethyl)-l-lysine (CML) western blot and glycation staining were used to directly identify glycation structures on the protein fractions on SDS-PAGE. Western blot was used to specify sRAGE and sIgE binding fractions. sRAGE binding was highest under wet-heated BLG independent of the presence of the milk sugar lactose. Under wet heating, high-molecular-weight aggregates were most potent and did not require the presence of CML to generate sRAGE binding ligands. In the dry system, sRAGE binding was observed only in the presence of lactose. sIgE binding affinity showed large individual differences and revealed four binding profiles. Dependent on the individual, sIgE binding decreased or increased by wet heating independent of the presence of lactose. Dry heating required the presence of lactose to show increased binding to aggregates in most individuals. This study highlights an important role of heating condition-dependent protein aggregation and glycation in changing the immunogenicity and antigenicity of cow's milk BLG.

The cysteine-rich region of a baculovirus VP91 protein contributes to the morphogenesis of occlusion bodies
Zhou, Fengqiao ; Kuang, Wenhua ; Wang, Xi ; Hou, Dianhai ; Huang, Huachao ; Sun, Xiulian ; Deng, Fei ; Wang, Hualin ; Oers, Monqiue M. van; Wang, Manli ; Hu, Zhihong - \ 2019
Virology 535 (2019). - ISSN 0042-6822 - p. 144 - 153.
Cysteine-rich region - Disulfide bond - HA76 - Occlusion body (OB) - Oral infection - P33 - Per os infectivity factor (PIF) - PIF8 - Polyhedra - VP91

The baculovirus core gene vp91 has been reported to be essential for nucleocapsid assembly and oral infection. Here, we studied the function of vp91 by analyzing its homologue, ha76, in Helicoverpa armigera nucleopolyhedrovirus (HearNPV). HA76 was expressed at the late stage of HearNPV infection; deletion of ha76 showed that the gene is required for budded virus production. A series of recombinants with truncated ha76 was constructed and analyzed in vitro and in vivo. The results showed that the region encoding the C-terminus of HA76 was essential for nucleocapsid assembly, whereas the N-terminal cysteine-rich region was responsible for oral infection. Electron microscope analyses further showed that the cysteine-rich region contributed to morphogenesis of occlusion bodies (OBs), with amino acids 136–223 of HA76 being critical for this function. The results revealed a novel function of VP91 and suggested that the impact on OB morphogenesis is partially related to oral infectivity.

Performance and microbial community analysis of Combined Denitrification and Biofloc Technology (CDBFT) system treating nitrogen-rich aquaculture wastewater
Li, Changwei ; Li, Jiawei ; Liu, Gang ; Deng, Yale ; Zhu, Songming ; Ye, Zhangying ; Shao, Yufang ; Liu, Dezhao - \ 2019
Bioresource Technology 288 (2019). - ISSN 0960-8524
Aquaculture wastewater - Biofloc technology - Denitrification - LED light - Microbial community

This study proposed two novel Combined Denitrification and Biofloc Technology (CDBFT) systems (one under blue LED light (L1) and the other without light (C1), each containing a denitrification (DE) reactor and a biofloc-based reactor) for the enhanced total nitrogen (TN) removal. Long-term operation (110 days) suggested that simultaneous nitrification and denitrification was achieved in both C1 and L1. Significantly higher total nitrogen removal efficiency (TNRE) was observed in L1-CDBFT (92.2%) than C1-CDBFT (87.5%, P < 0.05; after day 14). Further 24-hour nitrogen transformation test showed the boosted nitrate removal of L1-BFT than C1-BFT. High-throughput sequencing analysis revealed that phyla Rotifera and Nematoda which were indispensable for aquatic animal larviculture, were only found in L1-BFT. Nevertheless, CDBFT effluent from both systems was suitable for tilapia culture based on water quality, biofloc characteristics and tilapia survival rates. Overall, this study highlights the significance of developing CDBFT for TN removal especially under lights.

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota
Deng, Yale ; Xu, Xiangyang ; Yin, Xuwang ; Lu, Huifeng ; Chen, Guangshuo ; Yu, Jianhai ; Ruan, Yunjie - \ 2019
Applied Microbiology and Biotechnology 103 (2019)10. - ISSN 0175-7598 - p. 4241 - 4252.
Biofloc technology - Gut microbiota - Microbial community - Shrimp - Stock density

Biofloc technology is an efficient approach for intensive shrimp culture. However, the extent to which this process can influence the composition of intestinal microbial community is still unknown. Here, we surveyed the shrimp intestinal bacteria as well as the floc water from three biofloc systems with different stock densities. Our study revealed a similar variation trend in phylum taxonomy level between floc bacteria and gut microbiota. Microbial community varied notably in floc water from different stock densities, while a core genus with dominating relative abundance was detected in gut samples. Extensive variation was discovered in gut microbiota, but still clustered into groups according to stock density. Our results indicated that shrimp intestinal microbiota as well as bacteria aggregated in flocs assembled into distinct communities from different stock densities, and the intestinal communities were more similar with the surrounding environment as the increase of stock density and resulting high floc biomass. The high stock density changed the core gut microbiota by reducing the relative abundance of Paracoccus and increasing that of Nocardioides, which may negatively influence shrimp performance. Therefore, this study helps us to understand further bacteria and host interactions in biofloc system.

Understanding major NOM properties controlling its interactions with phosphorus and arsenic at goethite-water interface
Deng, Yingxuan ; Weng, Liping ; Li, Yongtao ; Ma, Jie ; Chen, Yali - \ 2019
Water Research 157 (2019). - ISSN 0043-1354 - p. 372 - 380.
Adsorption - Arsenate - Arsenite - Natural organic matter - Phosphate - Surface complexation model

Among natural organic matter (NOM), oxyanions and metal (hydr)oxides, a complicated interaction exists in natural aquatic and terrestrial systems and in waste waters. Effects of seven types of NOM (four humic acids (HA), three fulvic acids (FA)) that vary in properties on the adsorption of oxyanions, including phosphate, arsenate and arsenite, at goethite-water interface were quantitatively studied. Results show that the adsorption of oxyanions to goethite is decreased by the presence of NOM, especially for phosphate and arsenate at low pH. In general, the effects of the three FA are similar, which are more effective than HA in reducing oxyanion adsorption at low pH (<6). Differences were observed between the four HA in their competition with oxyanions. The adsorption of phosphate, arsenate and arsenite in the presence of NOM are well described with both the NOM-CD (CD: Charge Distribution) and LCD (Ligand and Charge Distribution) model. The NOM-CD model is relatively simple to use, whereas the LCD model can better reveal different factors in the interaction, including the spatial distribution of adsorbed NOM on oxide surface. According to these two models: site density of carboxylic groups, protonation constant of carboxylic groups, and particle size of NOM are major properties of NOM determining its effect on oxyanion adsorption to oxides. At relatively low loadings, morphological change of adsorbed NOM takes place, and the degree of morphological change of adsorbed NOM depends on the particle size, site density of carboxylic groups and aromaticity of NOM. The influence of particle size on the interaction becomes more important at higher NOM loadings. The results suggested that the fixation or removal efficiency of phosphate, arsenate and arsenite with iron oxides (e.g. goethite) can be significantly decreased by the presence of NOM, especially when NOM rich in acidic and aromatic groups.

Land tenure reform and grassland degradation in inner Mongolia, China
Liu, M. ; Dries, L.K.E. ; Heijman, W.J.M. ; Zhu, X. ; Deng, Xiangzheng ; Jikun Huang, - \ 2019
land tenure reform - privatisation - grassland degradation - fixed effects model - China
Since the start of the land tenure reform in the pastoral areas of China in the 1980s, grassland use rights have increasingly been assigned to individual households and subsequently more grasslands have been in private use. However, in the same period, most of the grasslands in China have experienced degradation. The question that this paper tries to address is whether the land tenure reform plays a significant role in grassland degradation. It is answered by an empirical analysis of the impact of land tenure reform on the changes in grassland condition, using data from 60 counties in Inner Mongolia between 1985 and 2008. Grassland condition is presented by grassland quantity and quality using spatial information based on remote sensing. The timing of the assignment of grassland use rights and the timing of the actual adoption of private use by households differ among counties. These timing differences and differences in grassland condition among counties allow disentangling the impact of the land tenure reform. A fixed effects model is used to control for climate, agricultural activity and the time-invariant heterogeneity among counties. The model results show that the private use of grasslands following the land tenure reform has had significantly negative effects on grassland quality and quantity in Inner Mongolia. Moreover, the negative effects did not disappear even after several years of experience with private use. In conclusion, our analysis reveals that the land tenure reform, namely privatisation of grassland use rights, is a significant driver of grassland degradation in Inner Mongolia in a long term, which presents "a tragedy of privatisation", as opposed to the well-known "tragedy of the commons".
Baculovirus per os infectivity factor complex : Components and assembly
Wang, Xi ; Shang, Yu ; Chen, Cheng ; Liu, Shurui ; Chang, Meng ; Zhang, Nan ; Hu, Hengrui ; Zhang, Fenghua ; Zhang, Tao ; Wang, Zhiying ; Liu, Xijia ; Lin, Zhe ; Deng, Fei ; Wang, Hualin ; Zou, Zhen ; Vlak, Just M. ; Wang, Manli ; Hu, Zhihong - \ 2019
Journal of Virology 93 (2019)6. - ISSN 0022-538X
Baculovirus - Entry - Per os infectivity factor - PIF complex - PIF9

Baculovirus entry into insect midgut cells is dependent on a multiprotein complex of per os infectivity factors (PIFs) on the envelopes of occlusion-derived virions (ODVs). The structure and assembly of the PIF complex are largely unknown. To reveal the complete members of the complex, a combination of blue native polyacrylamide gel electrophoresis, liquid chromatography-tandem mass spectrometry, and Western blotting was conducted on three different baculoviruses. The results showed that the PIF complex has a molecular mass of ~500 kDa and consists of nine PIFs, including a newly discovered member (PIF9). To decipher the assembly process, each pif gene was knocked out from the Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) genome individually by use of synthetic baculovirus technology, and the impact on PIF complex formation was investigated. Deletion of pif8 resulted in the formation of an ~400-kDa subcomplex. Deletion of pif0, -4, -6, -7, or -9 resulted in a subcomplex of ~230 kDa, but deletion of pif1, -2, or -3 abolished formation of any complex. Taken together, our data identified a core complex of ~230 kDa, consisting of PIF1, -2, and -3. This revised the previous knowledge that the core complex was about 170 kDa and contained PIF1 to -4. Analysis of the PIF complex in cellular fractions suggested that it is assembled in the cytoplasm before being transported to the nucleus and subsequently incorporated into the envelopes of ODVs. Only the full complex, not the subcomplex, is resistant to proteolytic attack, indicating the essentiality of correct complex assembly for oral infection. IMPORTANCE Entry of baculovirus into host insects is mediated by a per os infectivity factor (PIF) complex on the envelopes of occlusion-derived viruses (ODVs). Knowledge of the composition and structure of the PIF complex is fundamental to understanding its mode of action. By using multiple approaches, we determined the complete list of proteins (nine) in the PIF complex. In contrast to previous knowledge in the field, the core complex is revised to ~230 kDa and consists of PIF1 to -3 but not PIF4. Interestingly, our results suggest that the PIF complex is formed in the cytoplasm prior to its transport to the nucleus and subsequent incorporation into ODVs. Only the full complex is resistant to proteolytic degradation in the insect midgut, implying the critical role of the entire complex. These findings provide the baseline for future studies on the ODV entry mechanism mediated by the multiprotein complex.

Farm-level risk factors for bovine mastitis in Dutch automatic milking dairy herds
Deng, Z. ; Koop, G. ; Lam, T.J.G.M. ; Lans, I.A. van der; Vernooij, J.C.M. ; Hogeveen, H. - \ 2019
Journal of Dairy Science 102 (2019)5. - ISSN 0022-0302 - p. 4522 - 4535.
automatic milking system - mastitis - nonlinear principal component analysis - principal component regression - risk factor

Automatic milking systems (AMS) are installed on a growing number of dairy farms worldwide. Management to support good udder health might be different on farms with an AMS compared with farms milking with a conventional milking system, as risk factors for mastitis on farms using an AMS may differ. The aim of this study was to identify farm level factors associated with mastitis on Dutch dairy farms using an AMS. In 2008, risk factor data were collected using a questionnaire combined with on-farm recordings of cow, stall, and AMS hygiene on 135 farms. These risk factor data were linked to 4 udder-health-associated dependent variables: average herd somatic cell count (HeSCCav), variance of the average herd somatic cell count (SCC) on test days (HeSCCvar), the average proportion of new high SCC cases (NHiSCC), and the farmer-reported annual incidence rate of clinical mastitis (IRCM). We employed regression models using multiple imputation to deal with missing values. Due to the high dimensionality of the risk factor data, we also performed nonlinear principal component analysis (NLPCA) and regressed the dependent variables on the principal components (PC). Good hygiene of cows and of AMS were found to be related to a lower HeSCCav and less NHiSCC. Effective postmilking teat disinfection was associated with a lower NHiSCC. A higher bulk tank milk SCC threshold for farmers' action was related to more NHiSCC. Larger farm size was related to lower HeSCCvar but higher NHiSCC. Negative attitude of farmers to animal health, higher frequency of checking AMS, and more time spent on viewing computer data were all positively related to higher IRCM. An NLPCA with 3 PC explained 16.3% of the variance in the risk factor variables. Only the first 2 PC were associated with mastitis. The first PC reflected older and larger farms with poor cow hygiene and AMS hygiene, and was related to higher HeSCCav and NHiSCC, whereas the second PC reflected newly built smaller farms with poor cow hygiene and low milk production, and was associated with higher HeSCCvar and NHiSCC, but lower IRCM. Our study suggests that many of the risk factors on conventional milking system farms are applicable to AMS farms, specifically concerning hygiene of the cows and the milking machine, but on large AMS farms, udder health may need more attention than on smaller AMS farms. Multiple imputation is instrumental to deal with missing values and NLPCA is a useful technique to process high dimensional data in our study.

Hydrophobicity and aggregation, but not glycation, are key determinants for uptake of thermally processed β-lactoglobulin by THP-1 macrophages
Deng, Ying ; Govers, Coen ; Bastiaan-Net, Shanna ; Hulst, Nina van der; Hettinga, Kasper ; Wichers, Harry J. - \ 2019
Food Research International 120 (2019). - ISSN 0963-9969 - p. 102 - 113.
Aggregation - Glycation - Hydrophobicity - Thermal processing - THP-1 macrophage - Uptake - β-Lactoglobulin

The aim of this study is to investigate the immunological relevance of modifications of food protein structure due to thermal processing. We investigated the uptake of β-lactoglobulin, treated with 3 different processing methods, by THP-1 macrophages: wet heating (60 °C in solution) and high- or low-temperature (130 °C or 50 °C, respectively) dry heating, combined with either of 8 types of saccharides or without saccharide. The processing method that was applied significantly affected the uptake of BLG by THP-1 macrophages, while the type of saccharide only had an influence in high-temperature dry heated samples. A set of physicochemical parameters of processed samples was determined, to determine the samples' molecular weight, hydrophobicity, amyloid-like structure, surface charge and secondary structure. Analysis of protein structure alterations indicated the uptake to be linked to the wet heating processing method and percentage of α-helix structure, amyloid-like structures, polymers, and hydrophobicity. We hypothesize that both amyloid-like structures and molecular weight were related to the increased hydrophobicity and therefore postulate that the exposure of hydrophobic regions is the leading physicochemical characteristic for the observed uptake of wet heated BLG samples by THP-1 macrophages. This work demonstrates how differential thermal processing of foods, through protein modification, can have an impact on its interaction with the immune system.

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