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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    Transcriptome analysis of porcine granulosa cells in healthy and atretic follicles : Role of steroidogenesis and oxidative stress
    Meng, Li ; Wu, Zhenfang ; Zhao, Kun ; Tao, Jian ; Chit, Tam ; Zhang, Shouquan ; Wang, Chi Chiu ; Teerds, Katja - \ 2021
    Antioxidants 10 (2021)1. - ISSN 2076-3921 - p. 1 - 17.
    Antral follicular atresia - Oxidative stress - Steroidogenesis - Transcriptome profiles

    One of the main causes of female infertility is a deregulated antral follicular atresia, a process of which the underlying molecular mechanisms are largely unknown. Our objective was therefore to characterize the complex transcriptome changes in porcine granulosa cells of healthy antral (HA) and advanced antral atretic (AA) follicles, using ELISA and RNA-Seq followed by qRTPCR and immunohistochemistry. Granulosa cell RNA-Seq data revealed 2160 differentially expressed genes, 1483 with higher and 677 with lower mRNA concentrations in AA follicles. Bioinformatic analysis showed that the upregulated genes in AA follicles were highly enriched in inflammation and apoptosis processes, while the downregulated transcripts were mainly highlighted in the steroid biosynthesis pathway and response to oxidative stress processes including antioxidant genes (e.g., GSTA1, GCLC, GCLM, IDH1, GPX8) involved in the glutathione metabolism pathway and other redox-related genes (e.g., RRM2B, NDUFS4). These observations were confirmed by RT-qPCR and immunohistochemistry. Additionally, the granulosa cells of AA follicles express significantly stronger 8-OHdG immunostaining, a marker of oxidative DNA damage, implicating that oxidative stress may participate in follicular atresia. We hypothesize that the decrease in anti-apoptotic factors and steroid hormones coincides with increased oxidative stress markers and the expression of pro-apoptotic factors, all contributing to antral follicular atresia.

    Environmental drivers of Sphagnum growth in peatlands across the Holarctic region
    Bengtsson, Fia ; Rydin, Håkan ; Baltzer, Jennifer L. ; Bragazza, Luca ; Bu, Zhao Jun ; Caporn, Simon J.M. ; Dorrepaal, Ellen ; Flatberg, Kjell Ivar ; Galanina, Olga ; Gałka, Mariusz ; Ganeva, Anna ; Goia, Irina ; Goncharova, Nadezhda ; Hájek, Michal ; Haraguchi, Akira ; Harris, Lorna I. ; Humphreys, Elyn ; Jiroušek, Martin ; Kajukało, Katarzyna ; Karofeld, Edgar ; Koronatova, Natalia G. ; Kosykh, Natalia P. ; Laine, Anna M. ; Lamentowicz, Mariusz ; Lapshina, Elena ; Limpens, Juul ; Linkosalmi, Maiju ; Ma, Jin Ze ; Mauritz, Marguerite ; Mitchell, Edward A.D. ; Munir, Tariq M. ; Natali, Susan M. ; Natcheva, Rayna ; Payne, Richard J. ; Philippov, Dmitriy A. ; Rice, Steven K. ; Robinson, Sean ; Robroek, Bjorn J.M. ; Rochefort, Line ; Singer, David ; Stenøien, Hans K. ; Tuittila, Eeva Stiina ; Vellak, Kai ; Waddington, James Michael ; Granath, Gustaf - \ 2021
    Journal of Ecology 109 (2021)1. - ISSN 0022-0477 - p. 417 - 431.
    climate - global change - net primary production - nitrogen deposition - PAR - peat mosses - plant–climate interactions - structural equation model

    The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus Sphagnum—the main peat-former and ecosystem engineer in northern peatlands—remains unclear. We measured length growth and net primary production (NPP) of two abundant Sphagnum species across 99 Holarctic peatlands. We tested the importance of previously proposed abiotic and biotic drivers for peatland carbon uptake (climate, N deposition, water table depth and vascular plant cover) on these two responses. Employing structural equation models (SEMs), we explored both indirect and direct effects of drivers on Sphagnum growth. Variation in growth was large, but similar within and between peatlands. Length growth showed a stronger response to predictors than NPP. Moreover, the smaller and denser Sphagnum fuscum growing on hummocks had weaker responses to climatic variation than the larger and looser Sphagnum magellanicum growing in the wetter conditions. Growth decreased with increasing vascular plant cover within a site. Between sites, precipitation and temperature increased growth for S. magellanicum. The SEMs indicate that indirect effects are important. For example, vascular plant cover increased with a deeper water table, increased nitrogen deposition, precipitation and temperature. These factors also influenced Sphagnum growth indirectly by affecting moss shoot density. Synthesis. Our results imply that in a warmer climate, S. magellanicum will increase length growth as long as precipitation is not reduced, while S. fuscum is more resistant to decreased precipitation, but also less able to take advantage of increased precipitation and temperature. Such species-specific sensitivity to climate may affect competitive outcomes in a changing environment, and potentially the future carbon sink function of peatlands.

    Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro
    Hua, D. ; Zhao, Y. ; Nan, X. ; Xue, F. ; Wang, Y. ; Jiang, L. ; Xiong, B. - \ 2020
    Journal of Applied Microbiology (2020). - ISSN 1364-5072
    fermentation - gas production - glucogenic/lipogenic nutrients - in vitro - ruminal bacteria

    Aims: This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities. Methods and Results: Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others. Conclusions: When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R-7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio. Significance and Impact of the Study: The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end-products, gas production and bacterial composition via an in vitro technique.

    Fibrillarin evolution through the tree of life : Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of fibrillarin
    Pereira-Santana, Alejandro ; Gamboa-Tuz, Samuel David ; Zhao, Tao ; Schranz, Eric ; Vinuesa, Pablo ; Bayona, Andrea ; Rodríguez-Zapata, Luis C. ; Castano, Enrique - \ 2020
    PLoS Computational Biology 16 (2020)10. - ISSN 1553-734X

    Fibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and high conservation of fibrillarins, there little is known about the evolutionary dynamics of this small gene family. We applied a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins across the Tree of Life. We identified 1063 non-redundant FIB sequences across 1049 completely sequenced genomes from Viruses, Bacteria, Archaea, and Eukarya. FIB is a highly conserved single-copy gene through Archaea and Eukarya lineages, except for plants, which have a gene family expansion due to paleopolyploidy and tandem duplications. We found a high conservation of the FIB genomic context during plant evolution. Surprisingly, FIB in mammals duplicated after the Eutheria split (e.g., ruminants, felines, primates) from therian mammals (e.g., marsupials) to form two main groups of sequences, the FIB and FIB-like groups. The FIB-like group transposed to another genomic context and remained syntenic in all the eutherian mammals. This transposition correlates with differences in the expression patterns of FIB-like proteins and with elevated Ks values potentially due to reduced evolutionary constraints of the duplicated copy. Our results point to a unique evolutionary event in mammals, between FIB and FIB-like genes, that led to non-redundant roles of the vital processes in which this protein is involved.

    Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing
    Li, Jinghui ; Xing, Siyuan ; Zhao, Guiping ; Zheng, Maiqing ; Yang, Xinting ; Sun, Jiahong ; Wen, Jie ; Liu, Ranran - \ 2020
    BMC Genomics 21 (2020)1. - ISSN 1471-2164
    Breast muscle - Cell cluster - Intramuscular fat - RNA in situ hybridization - scRNA-seq

    Background: The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases—hyperplasia and hypertrophy. However, cell profiles corresponding to the two-phase muscle development have yet to be determined. Single-cell RNA-sequencing (scRNA-seq) can elucidate the cell subpopulations in tissue and capture the gene expression of individual cells, which can provide new insights into the myogenesis and intramuscular adipogenesis. Results: Ten cell clusters at the post-hatching developmental stage at Day 5 and seven cell clusters at the late developmental stage at Day 100 were identified in chicken breast muscles by scRNA-seq. Five myocyte-related clusters and two adipocyte clusters were identified at Day 5, and one myocyte cluster and one adipocyte cluster were identified at Day 100. The pattern of cell clustering varied between the two stages. The cell clusters showed clear boundaries at the terminal differentiation stage at Day 100; by contrast, cell differentiation was not complete at Day 5. APOA1 and COL1A1 were selected from up-regulated genes in the adipocyte cluster and found to be co-expressed with the ADIPOQ adipocyte marker gene in breast muscles by RNA in situ hybridization. Conclusions: This study is the first to describe the heterogeneity of chicken skeletal muscle at two developmental stages. The genes APOA1 and COL1A1 were identified as biomarkers for chicken intramuscular fat cells.

    Forensic soil source identification: comparing matching by color, vis-NIR spectroscopy and easily-measured physio-chemical properties
    Zeng, R. ; Rossiter, D.G. ; Zhao, Y.G. ; Li, D.C. ; Zhang, G.L. - \ 2020
    Forensic Science International 317 (2020). - ISSN 0379-0738
    Munsell color - RGB color - similarity analysis - spectral angle mapper
    This study evaluates to what degree soil samples associated in characteristic space are also close in geographical space, i.e., the possible location from which an unknown sample was obtained in a forensic investigation. The study compares similarity computed from Munsell colors, RGB colors, and full visible-near infrared (vis-NIR) spectra by the spectral angle mapper with similarity based on six easily-measured physio-chemical properties. The reference area is Anhui Province, China with three scales of datasets: provincial, county, and field. Ten diverse “unknown” samples were selected by the Kennard-Stone algorithm from the field-scale dataset and their matches in characteristic space from the several datasets were found by the different methods. The geographic distances of the matches to the “unknowns” were used to evaluate the source identification ability. When a detailed library with local samples is present, a limited set of physio-chemical properties achieved higher geographic accuracy than the color and spectral methods. However, with a regional library the spectral and color methods are superior. Distances in RGB space reveal finer differences than exact matching in Munsell space, but whole-spectra matching outperforms both, because of the rich information influenced by more soil properties than influencing color. We recommend the use of soil vis-NIR spectra as a priority indicator for forensic soil analysis because of its success in this study and its ability to work non-destructively on small quantities of soil.
    The potential roles of sponges in integrated mariculture
    Gökalp, Mert ; Mes, Daan ; Nederlof, Marit ; Zhao, Hongwei ; Merijn de Goeij, Jasper ; Osinga, Ronald - \ 2020
    Reviews in Aquaculture (2020). - ISSN 1753-5123
    DOM - integrated multitrophic aquaculture - sea cucumbers - seaweeds - sponge loop - sponges

    This mini-review evaluates the use of marine sponges in integrated culture systems, two decades after the idea was first proposed. It was predicted that the concept would provide a double benefit: sponges would grow faster under higher organic loadings, and filtration by sponges would improve water quality. It is promising that the growth of some commercially interesting sponges is indeed faster in organically enriched areas. The applicability of sponges as filters for undesired microorganisms has been confirmed in laboratory studies. However, upscaled farming studies need to be done to demonstrate the value of sponges for in situ bioremediation of sewage discharge or waste produced by fish cages. In addition, a new idea is presented – the use of sponges as an engine to convert dissolved organic matter (DOM) into particulate organic matter (POM) that can be consumed by deposit feeders through a chain of processes termed the sponge loop. A theoretical design of an integrated culture with seaweeds (Gracilaria sp.), sponges (Halisarca caerulea) and sea cucumbers (Apostichopus japonica) shows that 37% of the part of the primary production that is excreted by the seaweeds as DOM can be directly recovered in sponge biomass and a subsequent 12% in sea cucumber biomass after mediation (conversion of DOM to POM) by sponges. Hence, the total recovery of DOM into (sponge and sea cucumber) biomass within this IMTA is 49%.

    Clouds and Convective Self-Aggregation in a Multimodel Ensemble of Radiative-Convective Equilibrium Simulations
    Wing, Allison A. ; Stauffer, Catherine L. ; Becker, Tobias ; Reed, Kevin A. ; Ahn, Min Seop ; Arnold, Nathan P. ; Bony, Sandrine ; Branson, Mark ; Bryan, George H. ; Chaboureau, Jean Pierre ; De Roode, Stephan R. ; Gayatri, Kulkarni ; Hohenegger, Cathy ; Hu, Kuan ; Jansson, Fredrik ; Jones, Todd R. ; Khairoutdinov, Marat ; Kim, Daehyun ; Martin, Zane K. ; Matsugishi, Shuhei ; Medeiros, Brian ; Miura, Hiroaki ; Moon, Yumin ; Müller, Sebastian K. ; Ohno, Tomoki ; Popp, Max ; Prabhakaran, Thara ; Randall, David ; Rios-Berrios, Rosimar ; Rochetin, Nicolas ; Roehrig, Romain ; Romps, David M. ; Ruppert, James H. ; Satoh, Masaki ; Silvers, Levi G. ; Singh, Martin S. ; Stevens, Bjorn ; Tomassini, Lorenzo ; van Heerwaarden, Chiel C. ; Wang, Shuguang ; Zhao, Ming - \ 2020
    Journal of Advances in Modeling Earth Systems 12 (2020)9. - ISSN 1942-2466
    climate sensitivity - cloud feedbacks - clouds - convection - radiative-convective equilibrium - self-aggregation

    The Radiative-Convective Equilibrium Model Intercomparison Project (RCEMIP) is an intercomparison of multiple types of numerical models configured in radiative-convective equilibrium (RCE). RCE is an idealization of the tropical atmosphere that has long been used to study basic questions in climate science. Here, we employ RCE to investigate the role that clouds and convective activity play in determining cloud feedbacks, climate sensitivity, the state of convective aggregation, and the equilibrium climate. RCEMIP is unique among intercomparisons in its inclusion of a wide range of model types, including atmospheric general circulation models (GCMs), single column models (SCMs), cloud-resolving models (CRMs), large eddy simulations (LES), and global cloud-resolving models (GCRMs). The first results are presented from the RCEMIP ensemble of more than 30 models. While there are large differences across the RCEMIP ensemble in the representation of mean profiles of temperature, humidity, and cloudiness, in a majority of models anvil clouds rise, warm, and decrease in area coverage in response to an increase in sea surface temperature (SST). Nearly all models exhibit self-aggregation in large domains and agree that self-aggregation acts to dry and warm the troposphere, reduce high cloudiness, and increase cooling to space. The degree of self-aggregation exhibits no clear tendency with warming. There is a wide range of climate sensitivities, but models with parameterized convection tend to have lower climate sensitivities than models with explicit convection. In models with parameterized convection, aggregated simulations have lower climate sensitivities than unaggregated simulations.

    RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development
    Xing, Siyuan ; Liu, Ranran ; Zhao, Guiping ; Liu, Lu ; Groenen, Martien A.M. ; Madsen, Ole ; Zheng, Maiqing ; Yang, Xinting ; Crooijmans, Richard P.M.A. ; Wen, Jie - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    abdominal fat - chicken - intramuscular fat - tissue development - transcriptome

    Fat traits are important in the chicken industry where there is a desire for high intramuscular fat (IMF) and low abdominal fat. However, there is limited knowledge on the relationship between the dynamic status of gene expression and the body fat deposition in chicken. Transcriptome data were obtained from breast muscle and abdominal fat of female chickens from nine developmental stages (from embryonic day 12 to hatched day 180). In total, 8,545 genes in breast muscle and 6,824 genes in abdominal fat were identified as developmentally dynamic genes. Weighted correlation network analysis was used to identify gene modules and the hub genes. Twenty-one hub genes were identified, e.g., ENSGALG00000041996, which represents a candidate for high IMF, and CREB3L1, which relates to low abdominal fat weight. The transcript factor L3MBTL1 and the transcript factor cofactors TNIP1, HAT1, and BEND6 related to both high breast muscle IMF and low abdominal fat weight. Our results provide a resource of developmental transcriptome profiles in chicken breast muscle and abdominal fat. The candidate genes can be used in the selection for increased IMF content and/or a decrease in abdominal fat weight which would contribute to the improvement of these traits.

    Urbanization-driven changes in land-climate dynamics : A case study of Haihe River Basin, China
    Li, Zhouyuan ; Xu, Yanjie ; Sun, Yingbao ; Wu, Mengfan ; Zhao, Bin - \ 2020
    Remote Sensing 12 (2020)17. - ISSN 2072-4292
    Albedo - Cloud - Land surface temperature - Land use and cover change (LUCC) - Land-climate - NDVI - Precipitation - Structural equation model (SEM) - Urbanization

    Urbanization changes the land surface environment, which alters the regional climate system. In this study, we took the Haihe River Basin in China as a case study area, as it is highly populated and experienced rapid urbanization from 2000-2015. We investigated how land use and cover change (LUCC) was driven by urban land development affects land-climate dynamics. From 2000-2015, we collected data from the land use and cover database, the remote sensing database of the Moderate Resolution Imaging Spectroradiometer (MODIS) series, and the meteorological database to process and generate regional datasets for LUCC maps. We organized data by years aligned with the selected indicators of land surface, normalized difference vegetation index (NDVI), albedo, and land surface temperature (LST), as well as of regional climate, cloud water content (CWC), and precipitation (P). The assembled datasets were processed to perform statistical analysis and conduct structural equation modelling (SEM). Based on eco-climatology principles and the biophysical process in the land-climate dynamics, we made assumptions on how the indicators connected to each other. Moreover, we testified and quantified them in SEM. LUCC results found that from 2000-2015 the urban area proportion increased by 214% (2.20-6.91%), while the agricultural land decreased by 7.2% (53.05-49.25%) and the forest increased by 4.3% (10.02-10.45%), respectively. This demonstrated how cropland intensification and afforestation happened in the urbanizing basin. SEM results showed that the forest had both positive and negative effects on the regional hydrological cycle. The agricultural land, grassland, and shrub had indirect effects on the P via different biophysical functions of LST. The overall effects of urbanization on regional precipitation was positive (pathway correlation coefficient = 0.25). The interpretation of how urbanization drives LUCC and alters regional climate were herein discussed in different aspects of socioeconomic development, biophysical processes, and urbanization-related atmospheric effects. We provided suggestions for further possible research on monitoring and assessment, putting forth recommendations to advance sustainability via land planning and management, including agricultural land conservation, paying more attention to the quality growth of forest rather than the merely area expansion, integrating the interdisciplinary approach, and assessing climatic risk for extreme precipitation and urban flooding.

    UDP-glucosyltransferase UGT84B1 regulates the levels of indole-3-acetic acid and phenylacetic acid in Arabidopsis
    Aoi, Yuki ; Hira, Hayao ; Hayakawa, Yuya ; Liu, Hongquan ; Fukui, Kosuke ; Dai, Xinhua ; Tanaka, Keita ; Hayashi, Ken Ichiro ; Zhao, Yunde ; Kasahara, Hiroyuki - \ 2020
    Biochemical and Biophysical Research Communications 532 (2020)2. - ISSN 0006-291X - p. 244 - 250.
    Auxin - Indole-3-acetic acid - Metabolism - Phenylacetic acid - UDP-Glucosyltransferase

    Auxin is a key plant growth regulator for diverse developmental processes in plants. Indole-3-acetic acid (IAA) is a primary plant auxin that regulates the formation of various organs. Plants also produce phenylacetic acid (PAA), another natural auxin, which occurs more abundantly than IAA in various plant species. Although it has been demonstrated that the two auxins have distinct transport characteristics, the metabolic pathways and physiological roles of PAA in plants remain unsolved. In this study, we investigated the role of Arabidopsis UDP-glucosyltransferase UGT84B1 in IAA and PAA metabolism. We demonstrated that UGT84B1, which converts IAA to IAA-glucoside (IAA-Glc), can also catalyze the conversion of PAA to PAA-glucoside (PAA-Glc), with a higher catalytic activity in vitro. Furthermore, we showed a significant increase in both the IAA and PAA levels in the ugt84b1 null mutants. However, no obvious developmental phenotypes were observed in the ugt84b1 mutants under laboratory growth conditions. Moreover, the overexpression of UGT84B1 resulted in auxin-deficient root phenotypes and changes in the IAA and PAA levels. Our results indicate that UGT84B1 plays an important role in IAA and PAA homeostasis in Arabidopsis.

    Effects of long-term super absorbent polymer and organic manure on soil structure and organic carbon distribution in different soil layers
    Yang, Yonghui ; Wu, Jicheng ; Zhao, Shiwei ; Gao, Cuimin ; Pan, Xiaoying ; Tang, Darrell W.S. ; Ploeg, Martine van der - \ 2020
    Soil & Tillage Research 206 (2020). - ISSN 0167-1987
    Contribution rate of organic carbon - Organic manure - Soil organic carbon - Soil structure - Super absorbent polymer

    Super absorbent polymer (SAP) and organic manure (OM) may improve soil structure and change soil organic carbon (SOC) composition and agroecosystem functioning. However, the understanding of the effects of SAP and OM on SOC composition, specifically in deeper soil layers, is still not clear. The objectives of this study were to examine the effects of long-term application of SAP and OM (8 years) on changes in SOC and soil structure down to a soil depth of 100 cm. Therefore, in order to investigate the stability of soil structure and the distribution of organic carbon at different soil depths (0-10 cm, 10-20 cm,…, 90-100 cm) under long-term application of SAP, OM, and a control treatment, soil structure and soil organic carbon content were analyzed in mixed soil samples and undisturbed soil samples. The results indicated that with depth, the proportion of large aggregates (0.5-2.0 mm) decreased gradually, while the proportion of small aggregates (<0.25 mm) increased gradually. Compared with the control, SAP treatment was conducive to the increment of>0.5 mm soil aggregates in the 0-30 cm and 40-60 cm soil layers (P < 0.05) and 0.25-0.5 mm in the 0-50 cm soil layer (P < 0.05), and while the OM treatment had the same effect in the 0-30 cm soil layer (P < 0.05). The total organic carbon content (TOC) and labile organic carbon content (LOC) of bulk soil increased (0-20 cm) initially with depth, and then decreased (20-70 cm) approximately. In the 0-50 cm soil layer, the TOC and LOC under SAP treatment were higher than those under OM treatment. The SAP treatment was more beneficial to the increase of the TOC and LOC of 0.5-2.0 mm and 0.25-0.5 mm aggregates in the 10-40 cm soil layer compared with the control and OM treatment (P < 0.05). The SAP treatment was also more beneficial in increasing the contribution rate of organic carbon (CROC) in> 0.5 mm aggregates in 0-40 cm soil depth, while the OM treatment was more beneficial in increasing the CROC of > 0.5 mm aggregates in 0-30 cm soil depth. The SAP treatment improved the stability of the soil structure in 0-30 cm and 40-60 cm depths, and the OM treatment had the same effect in the 0-30 cm depth. Compared with the control and OM treatments, SAP treatment has shown to be the most beneficial in improving soil structure and increasing organic carbon content.

    Rapid high-throughput determination of major components and amino acids in a single peanut kernel based on portable near-infrared spectroscopy combined with chemometrics
    Yu, Hongwei ; Liu, Hongzhi ; Erasmus, Sara Wilhelmina ; Zhao, Simeng ; Wang, Qiang ; Ruth, S.M. van - \ 2020
    Industrial Crops and Products 158 (2020)158. - ISSN 0926-6690
    The quality traits of peanuts (Arachis hypogaea L.) are fundamental to the whole peanut industry. However, many common analyses require the sample to be brought to the laboratory. Therefore, this research explores the feasibility of portable near-infrared spectroscopy combined with a single detection accessory to analyse the composition of peanuts in a single seed level quantitatively. The single detection accessory was specifically designed for spectral data collection considering the internal and external characteristics of single peanuts. Confocal laser scanning microscopy revealed that the oil body and protein body were randomly distributed at cell of single peanuts. The external characteristics of single peanuts were also determined and considered length (11.32–24.25 mm) and width (7.49–12.25 mm). The chemical compositional data (i.e. fat, sucrose, protein, and 16 amino acids) were determined by conventional wet-chemical methods and showed large variation. Principal component analysis on the compositional data showed that peanuts with higher fat contents usually have higher hydrophobic amino acids contents, lower sucrose contents, and lower protein contents. The composition prediction models of single peanuts were estimated using partial least squares regression models that were integrated with different spectral pre-treatments and validated by external sets. The results showed that the prediction models have good performance with a correlation coefficient above 0.88 (calibration) and 0.83 (prediction) and a residual prediction deviation above 1.5 except for a few indicators. Overall, the portable near-infrared spectroscopy offered reliable methods to assess the major components and amino acids quantitatively in a single peanut, which will improve the raw material quality in the peanut industry through the simultaneous and short-term determination of multiple indicators.
    Purification and characterization of bacteriocin produced by Lactobacillus rhamnosus zrx01
    Zhao, Ruixiang ; Lu, Yanqing ; Ran, Junjian ; Li, Gang ; Lei, Shuang ; Zhu, Yang ; Xu, Baocheng - \ 2020
    Food Bioscience 38 (2020). - ISSN 2212-4292
    Antibacterial stability - Bacteriocin - Lactobacillus rhamnosus zrx01

    The bacteriocin-zrx01 produced by Lactobacillus rhamnosus zrx01 was purified, its basic biochemical characteristics and bacterial antibacterial sensitivity were studied. The bacteriocin-zrx01 was separated and purified using ethyl acetate, AKTA purifier™ 10 protein purifier with HiTrap™ Capto™ Q anion exchange chromatography and Superdex™ 75 10/300 GL gel chromatography. The purity of bacteriocin-zrx01 was analyzed using high performance liquid chromatography. The sensitivity to temperature, pH and enzymes of the purified bacteriocin-zrx01 was measured as the diameter of the antimicrobial ring. The results showed that the purified bacteriocin-zrx01 bacterial antibacterial activity was good, and the specific vitality was raised from the original fermentation broth at 625 to 5330 AU/mg. The bacteriocin-zrx01 had a higher stability at pH 3–9, and the antibacterial activity was the strongest at pH 4. When pH was 9, it still retained 86% of the antibacterial activity of the control group. Bacteriocin-zrx01 was cold-stable at −70 and −20 °C for 30 min. It still retained 57% antimicrobial activity compared with the control after being autoclaved at 121 °C for 30 min. Some enzymes, such as protease K, neutral protease, trypsin, thrombin, alkaline protease and papain, affected its antibacterial activity, but it was sensitive to pepsin, and the diameter of the antimicrobial ring decreased by 50% after 2 h of pepsin treatment. These results showed that the bacteriocin-zrx01 produced by Lactobacillus rhamnosus zrx01 might have a potential as a natural food preservative, although in vivo studies are needed.

    The impact of land transfer and farmers’ knowledge of farmland protection policy on pro-environmental agricultural practices : The case of straw return to fields in Ningxia, China
    Cao, Hui ; Zhu, Xueqin ; Heijman, Wim ; Zhao, Kai - \ 2020
    Journal of Cleaner Production 277 (2020). - ISSN 0959-6526
    Agricultural sustainable development - China - Knowledge of farmland protection policy - Land transfer - Pro-environmental agricultural practices

    Farmers’ pro-environmental agricultural practices (PAPs) are important measures to limit agricultural pollution and improve farmland quality. Given the positive externality of PAPs, the Chinese government has proposed a series of farmland protection policies to encourage farmers to implement PAPs. However, land transfer, an increasingly common phenomenon, may affect the effectiveness of policies. This study aims to explore how farmers’ PAPs have been affected by land transfer and farmers’ knowledge of farmland protection policy (KFPP). A systematic theoretical framework for this relation is developed. The probit model is applied to empirically investigate the relationship between land transfer, KFPP and the PAP of straw return to fields based on data collected from 400 farmers in Ningxia Province in China. The findings reveal that farmers’ KFPP has a positive effect on PAPs. Rented-in land has a positive effect on PAPs, while rented-out land has a negative effect, which is significantly reduced with the adjustment effect of KFPP on land transfer. Our analysis provides policy implications for the successful implementation of PAPs. The positive effect of rented-in land and the negative effect of land fragmentation on PAPs suggest the importance of policies promoting land consolidation by incorporating plot-connecting interventions in the land rental market. The positive and significant effect of KFPP on PAPs suggests further enhancing farmers’ knowledge of farmland protection policy, for example, by improving information channels and extension services.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Karolinska Institute
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics
    Background Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods We performed meta-analysis of Illumina’s HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4–18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. Results We identified 8899 CpGs in cord blood that were associated with gestational age (range 27–42 weeks), at Bonferroni significance, P
    Height-diameter allometric relationships for seedlings and trees across China
    Zhang, Wei Ping ; Zhao, Lei ; Larjavaara, Markku ; Morris, E.C. ; Sterck, Frank J. ; Wang, Gen Xuan - \ 2020
    Acta Oecologica-International Journal of Ecology 108 (2020). - ISSN 1146-609X
    Allometric exponent - Canopy species - Gymnosperm - Scaling relationships - Seedling - Understory species

    Height–diameter allometric (H-D) relationships play an important role in the light capture and stability of a tree, and it is poorly understood whether the relationships changes with growth stages or functional groups along a large scale environmental gradients. We present a comparative study of H-D relationships of 6810 seedlings and 19,707 trees from about 1000 species in 9 different sites across China. We showed that allometric exponents for seedlings and trees differ between different sites and do not represent a single, constant theoretical value (e.g. 2/3, 1/2 or 1). Seedlings had greater exponents than trees in most sites. The exponents varied between canopy and understory trees in 5 sites, while were indistinguishable from each other in the remaining 4 sites. Canopy-tree seedlings had smaller exponents than understory-tree seedlings in 3 sites but had indistinguishable exponents in the other 6 sites. Gymnosperm trees had exponents greater than or indistinguishable from angiosperm trees. Elevation alone, or together with mean temperature of the warmest month explained variation of tree allometries for canopy-tree and understory-tree seedlings. The exponents of canopy trees decreased with mean annual precipitation. Our results do not support the predictions from metabolic scaling theory or biomechanical models that height–diameter allometries are invariant. Our study provides insight into how ontogeny, adult stature, phyletic affiliations and environmental limitations affect height–diameter allometric relationships at biogeographical scales.

    Yield components, reproductive allometry and the tradeoff between grain yield and yield stability in dryland spring wheat
    Du, Yan Lei ; Xi, Yue ; Cui, Ting ; Anten, Niels P.R. ; Weiner, Jacob ; Li, Xinmao ; Turner, Neil C. ; Zhao, Yi Min ; Li, Feng Min - \ 2020
    Field Crops Research 257 (2020). - ISSN 0378-4290
    Risk reduction - Smallholder farms - Variety screening - Wheat breeding - Yield stability

    Yield improvement for smallholder farmers in developing countries via crop breeding has been slow, in part because breeders have focused primarily on higher yields rather than stability of yield across environments. We investigated the relationships between (i) grain yield and yield-component traits, (ii) grain yield and yield stability, and (iii) reproductive (R) and vegetative (V) biomass in a field experiment with 18 spring wheat genotypes varying from landraces to recently-released breeding lines in a semiarid region under three different levels of precipitation. Genotypic differences in grain yield varied with the environment. The relationship between grain yield and yield components was also dependent on the environment, making it difficult to identify early-screening parameters for use in breeding programs. A genotype main effects and genotype by environment interaction effect analysis (GGE) showed a negative relationship between mean grain yield and yield stability across environments. There were significant differences among genotypes in the allometric exponent of the R-V relationship (slope of the log R – log V relationship). For the three highest yielding but less stable genotypes, this slope value was > 1, while the five lowest yielding, but more stable genotypes, it was < 1. We hypothesize that the tradeoff between grain yield and yield stability reported here is biologically constrained and cannot be eliminated through breeding. Therefore, a balance between yield stability and high yield should be considered in future wheat breeding programs for smallholder farmers, rather than attempting to improve both.

    Assessing the combined toxicity effects of three neonicotinoid pesticide mixtures on human neuroblastoma SK-N-SH and lepidopteran Sf-9 cells
    Cheng, Lin ; Lu, Yangyang ; Zhao, Zhihui ; Hoogenboom, Ron L.A.P. ; Zhang, Qicai ; Liu, Xing ; Song, Wei ; Guan, Shuhui ; Song, Weiguo ; Rao, Qinxiong - \ 2020
    Food and Chemical Toxicology 145 (2020). - ISSN 0278-6915
    Combined toxicity - Human neuroblastoma cell line SK-N-SH - Lepidopteran (Spodoptera frugiperda) cell line Sf-9 - Mixtures - Neonicotinoid pesticides

    Neonicotinoid insecticides have been widely used in plant protection against pests worldwide. Generally, more than one neonicotinoids are detected in plants and foods, and such mixtures may show combined toxicity and increase the risk for both insects and higher organisms. In this study, the combined toxicity of imidacloprid (IM), acetamiprid (AC) and thiamethoxam (TH) was investigated using human neuroblastoma cell line (SK-N-SH) and lepidopteran cell line (Sf-9). Results showed that binary and ternary mixtures could enhance the inhibition of growth of both SK-N-SH and Sf-9 cells at low doses. In SK-N-SH cells, based on CompuSyn software analysis, all the mixtures of IM+AC, IM+TH, AC+TH and IM+AC+TH showed synergistic effects at concentrations < 50 mg/L, but IM+AC, IM+TH showed antagonistic effects at higher concentrations. For Sf-9 cells, all mixtures revealed synergistic effects at low concentrations (< 0.1 mg/L) except IM+AC, showing antagonism at higher concentrations (> 0.5 mg/L). The toxicity thresholds of mixtures denoted by BMDL10 values were all lower than those for single pesticides and the combined BMDL10 value of AC+TH was the lowest one. It is concluded that the co-occurrence of several neonicotinoid insecticides may enhance their toxicity and aggravate the health risk for both insects and human.

    Characteristics of circular rna expression profiles of porcine granulosa cells in healthy and atretic antral follicles
    Meng, Li ; Teerds, Katja ; Tao, Jian ; Wei, Hengxi ; Jaklofsky, Marcel ; Zhao, Zhihong ; Liang, Yaodi ; Li, Li ; Wang, Chi Chiu ; Zhang, Shouquan - \ 2020
    International Journal of Molecular Sciences 21 (2020)15. - ISSN 1422-0067 - 25 p.
    Antral follicular atresia - CircRNA expression profiles - Granulosa cell apoptosis

    Circular RNAs (circRNAs) are thought to play essential roles in multiple biological processes, including apoptosis, an important process in antral follicle atresia. We aimed to investigate the potential involvement of circRNAs in granulosa cell apoptosis and thus antral follicle atresia. CircRNA expression profiles were generated from porcine granulosa cells isolated from healthy antral (HA) and atretic antral (AA) follicles. Over 9632 circRNAs were identified, of which 62 circRNAs were differentially expressed (DE-circRNAs). Back-splicing, RNase R resistance, and stability of DE-circRNAs were validated, and miRNA binding sites and related target genes were predicted. Two exonic circRNAs with low false discovery rate (FDR) high fold change, miRNA binding sites, and relevant biological functions—circ_CBFA2T2 and circ_KIF16B—were selected for further characterization. qRT-PCR and linear regression analysis confirmed expression and correlation of the targeted genes—the antioxidant gene GCLC (potential target of circ_CBFA2T2) and the apoptotic gene TP53 (potential target of circ_KIF16B). Increased mRNA content of TP53 in granulosa cells of AA follicles was further confirmed by strong immunostaining of both p53 and its downstream target pleckstrin homology like domain family a member 3 (PHLDA3) in AA follicles compared to negligible staining in granulosa cells of HA follicles. Therefore, we concluded that aberrantly expressed circRNAs presumably play a potential role in antral follicular atresia.

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