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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    Can pedotransfer functions based on environmental variables improve soil total nutrient mapping at a regional scale?
    Song, Xiao Dong ; Rossiter, David G. ; Liu, Feng ; Wu, Hua Yong ; Zhao, Xiao Rui ; Cao, Qi ; Zhang, Gan Lin - \ 2020
    Soil & Tillage Research 202 (2020). - ISSN 0167-1987
    Digital soil mapping - Random forest - Regression analysis - Total nitrogen - Total phosphorus - Total potassium

    Numerous pedotransfer functions (PTFs) have been developed to predict the soil properties of interest from other soil properties and, less commonly, from environmental variables. However, only a few PTFs have been developed to predict soil nutrients using environmental variables and to extrapolate them to characterize spatial soil variations at a regional scale. In this study, we attempted to develop PTFs for the total nitrogen (TN), total phosphorus (TP) and total potassium (TK) concentrations in three typical pedo-climatic areas of China (Fujian Province, Jiangsu Province and Qilian Mountains) with diverse climate, terrain and soil types. A series of linear PTFs were developed to quantify the effect of terrain and climate on the predictive relations between the soil nutrients and other measured soil properties and environmental variables. In addition, digital soil mapping (DSM) based on the random forest (RF) technique was performed to test the hypothesis that the best-fit PTFs could be extrapolated, based on soil maps and environmental variables, to describe regional soil variations in the soil nutrients. The root mean square errors (RMSEs) of the best-fit PTFs for TN, TP and TK ranged from 0.21 to 0.79 g kg−1, 0.20 to 0.58 g kg−1, and 3.68 to 5.00 g kg−1, respectively. Different RMSEs were produced by DSM, namely 0.37-1.89 g kg−1, 0.19−0.56 g kg−1 and 3.79-4.83 g kg−1 for TN, TP and TK, respectively. PTFs provided a sound basis for database compilation if the soil properties were highly correlated. However, the extrapolation of best-fit PTFs to regional scales yielded greater errors than those produced by DSM. The comparison results reveal the limitations of PTFs and suggest that their performance could be improved by using environmental covariates or by fitting data in areas with relatively homogeneous soil landscapes. The DSM techniques may provide satisfactory alternatives to predict soil data at both regional and plot scales.

    Collateral damage? Small-scale fisheries in the global fight against IUU fishing
    Song, Andrew M. ; Scholtens, Joeri ; Barclay, Kate ; Bush, Simon R. ; Fabinyi, Michael ; Adhuri, Dedi S. ; Haughton, Milton - \ 2020
    Fish and Fisheries (2020). - ISSN 1467-2960
    catch certification - developing countries - fisheries governance - maritime security - organized crime - seafood trade

    Concern over illegal, unreported and unregulated (IUU) fishing has led to a number of policy, trade and surveillance measures. While much attention has been given to the impact of IUU regulation on industrial fleets, recognition of the distinct impacts on small-scale fisheries is conspicuously lacking from the policy and research debate. In this paper, we outline three ways in which the application of IUU discourse and regulation undermines small-scale fisheries. First, the mainstream construction of “illegal,” “unreported” and “unregulated” fishing, and also the categorical use of “IUU” in an all-inclusive sense, disregards the diversity, legitimacy and sustainability of small-scale fisheries practices and their governing systems. Second, we explore how the recent trade-related measures to counter IUU fishing mask and reinforce existing inequalities between different sectors and countries, creating an unfair burden on small-scale fisheries and countries who depend on them. Third, as IUU fishing is increasingly approached as “organized crime,” there is a risk of inappropriately targeting small-scale fisheries, at times violently. Reflecting on these three trends, we propose three strategies by which a more sensitive and ultimately more equitable incorporation of small-scale fisheries can be supported in the global fight against IUU fishing.

    Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild
    Pascoal, Sonia ; Risse, Judith E. ; Zhang, Xiao ; Blaxter, Mark ; Cezard, Timothee ; Challis, Richard J. ; Gharbi, Karim ; Hunt, John ; Kumar, Sujai ; Langan, Emma ; Liu, Xuan ; Rayner, Jack G. ; Ritchie, Michael G. ; Snoek, Basten L. ; Trivedi, Urmi ; Bailey, Nathan W. - \ 2020
    Evolution Letters 4 (2020)1. - ISSN 2056-3744 - p. 19 - 33.
    Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound‐producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome‐wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking.
    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses
    Murphy, Neil ; Carreras-Torres, Robert ; Song, Mingyang ; Chan, Andrew T. ; Martin, Richard M. ; Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Bradbury, Kathryn E. ; Besevic, Jelena ; Rinaldi, Sabina ; Riboli, Elio ; Cross, Amanda J. ; Travis, Ruth C. ; Agnoli, Claudia ; Albanes, Demetrius ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Brenner, Hermann ; Buchanan, Daniel D. ; Onland-Moret, N.C. ; Burnett-Hartman, Andrea ; Campbell, Peter T. ; Casey, Graham ; Castellví-Bel, Sergi ; Chang-Claude, Jenny ; Chirlaque, María Dolores ; Chapelle, Albert de la; English, Dallas ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hsu, Li ; Huang, Wen Yi ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Kweon, Sun Seog ; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Martín, Vicente ; Milne, Roger L. ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Ogino, Shuji ; Ose, Jennifer ; Perduca, Vittorio ; Phipps, Amanda I. ; Platz, Elizabeth A. ; Potter, John D. ; Qu, Conghui ; Rennert, Gad ; Sakoda, Lori C. ; Schafmayer, Clemens ; Schoen, Robert E. ; Slattery, Martha L. ; Tangen, Catherine M. ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Visvanathan, Kala ; Vodicka, Pavel ; Vodickova, Ludmila ; Vymetalkova, Veronika ; Wang, Hansong ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Zheng, Wei ; Peters, Ulrike ; Gunter, Marc J. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1300 - 1312.e20.
    CRC - GWAS - Risk Factors - Signal Transduction

    Background & Aims: Human studies examining associations between circulating levels of insulin-like growth factor 1 (IGF1) and insulin-like growth factor binding protein 3 (IGFBP3) and colorectal cancer risk have reported inconsistent results. We conducted complementary serologic and Mendelian randomization (MR) analyses to determine whether alterations in circulating levels of IGF1 or IGFBP3 are associated with colorectal cancer development. Methods: Serum levels of IGF1 were measured in blood samples collected from 397,380 participants from the UK Biobank, from 2006 through 2010. Incident cancer cases and cancer cases recorded first in death certificates were identified through linkage to national cancer and death registries. Complete follow-up was available through March 31, 2016. For the MR analyses, we identified genetic variants associated with circulating levels of IGF1 and IGFBP3. The association of these genetic variants with colorectal cancer was examined with 2-sample MR methods using genome-wide association study consortia data (52,865 cases with colorectal cancer and 46,287 individuals without [controls]) Results: After a median follow-up period of 7.1 years, 2665 cases of colorectal cancer were recorded. In a multivariable-adjusted model, circulating level of IGF1 associated with colorectal cancer risk (hazard ratio per 1 standard deviation increment of IGF1, 1.11; 95% confidence interval [CI] 1.05–1.17). Similar associations were found by sex, follow-up time, and tumor subsite. In the MR analyses, a 1 standard deviation increment in IGF1 level, predicted based on genetic factors, was associated with a higher risk of colorectal cancer risk (odds ratio 1.08; 95% CI 1.03–1.12; P = 3.3 × 10–4). Level of IGFBP3, predicted based on genetic factors, was associated with colorectal cancer risk (odds ratio per 1 standard deviation increment, 1.12; 95% CI 1.06–1.18; P = 4.2 × 10–5). Colorectal cancer risk was associated with only 1 variant in the IGFBP3 gene region (rs11977526), which also associated with anthropometric traits and circulating level of IGF2. Conclusions: In an analysis of blood samples from almost 400,000 participants in the UK Biobank, we found an association between circulating level of IGF1 and colorectal cancer. Using genetic data from 52,865 cases with colorectal cancer and 46,287 controls, a higher level of IGF1, determined by genetic factors, was associated with colorectal cancer. Further studies are needed to determine how this signaling pathway might contribute to colorectal carcinogenesis.

    Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics
    Song, Jinzhao ; Hegge, Jorrit W. ; Mauk, Michael G. ; Chen, Junman ; Till, Jacob E. ; Bhagwat, Neha ; Azink, Lotte T. ; Peng, Jing ; Sen, Moen ; Mays, Jazmine ; Carpenter, Erica L. ; Oost, John van der; Bau, Haim H. - \ 2020
    Nucleic acids research 48 (2020)4. - ISSN 0305-1048 - p. e19 - e19.

    Detection of disease-associated, cell-free nucleic acids in body fluids enables early diagnostics, genotyping and personalized therapy, but is challenged by the low concentrations of clinically significant nucleic acids and their sequence homology with abundant wild-type nucleic acids. We describe a novel approach, dubbed NAVIGATER, for increasing the fractions of Nucleic Acids of clinical interest Via DNA-Guided Argonaute from Thermus thermophilus (TtAgo). TtAgo cleaves specifically guide-complementary DNA and RNA with single nucleotide precision, greatly increasing the fractions of rare alleles and, enhancing the sensitivity of downstream detection methods such as ddPCR, sequencing, and clamped enzymatic amplification. We demonstrated 60-fold enrichment of the cancer biomarker KRAS G12D and ∼100-fold increased sensitivity of Peptide Nucleic Acid (PNA) and Xenonucleic Acid (XNA) clamp PCR, enabling detection of low-frequency (<0.01%) mutant alleles (∼1 copy) in blood samples of pancreatic cancer patients. NAVIGATER surpasses Cas9-based assays (e.g. DASH, Depletion of Abundant Sequences by Hybridization), identifying more mutation-positive samples when combined with XNA-PCR. Moreover, TtAgo does not require targets to contain any specific protospacer-adjacent motifs (PAM); is a multi-turnover enzyme; cleaves ssDNA, dsDNA and RNA targets in a single assay; and operates at elevated temperatures, providing high selectivity and compatibility with polymerases.

    Natural Variation in Portuguese Common Bean Germplasm Reveals New Sources of Resistance Against Fusarium oxysporum f. sp. phaseoli and Resistance-Associated Candidate Genes
    Leitão, Susana T. ; Malosetti, Marcos ; Song, Qijan ; Eeuwijk, Fred van; Rubiales, Diego ; Vaz Patto, Maria Carlota - \ 2020
    Phytopathology 110 (2020)3. - ISSN 0031-949X - p. 633 - 647.
    Fusarium wilt - genetics and resistance - Phaseolus vulgaris

    Common bean (Phaseolus vulgaris) is one of the most consumed legume crops in the world, and Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. phaseoli, is one of the major diseases affecting its production. Portugal holds a very promising common bean germplasm with an admixed genetic background that may reveal novel genetic resistance combinations between the original Andean and Mesoamerican gene pools. To identify new sources of Fusarium wilt resistance and detect resistance-associated single-nucleotide polymorphisms (SNPs), we explored, for the first time, a diverse collection of the underused Portuguese common bean germplasm by using genome-wide association analyses. The collection was evaluated for Fusarium wilt resistance under growth chamber conditions, with the highly virulent F. oxysporum f. sp. phaseoli strain FOP-SP1 race 6. Fourteen of the 162 Portuguese accessions evaluated were highly resistant and 71 intermediate. The same collection was genotyped with DNA sequencing arrays, and SNP-resistance associations were tested via a mixed linear model accounting for the genetic relatedness between accessions. The results from the association mapping revealed nine SNPs associated with resistance on chromosomes Pv04, Pv05, Pv07, and Pv08, indicating that Fusarium wilt resistance is under oligogenic control. Putative candidate genes related to phytoalexin biosynthesis, hypersensitive response, and plant primary metabolism were identified. The results reported here highlight the importance of exploring underused germplasm for new sources of resistance and provide new genomic targets for the development of functional markers to support selection in future disease resistance breeding programs.

    Rhizosphere protists are key determinants of plant health
    Xiong, Wu ; Song, Yuqi ; Yang, Keming ; Gu, Yian ; Wei, Zhong ; Kowalchuk, George A. ; Xu, Yangchun ; Jousset, Alexandre ; Shen, Qirong ; Geisen, Stefan - \ 2020
    Microbiome 8 (2020)1. - ISSN 2049-2618
    Pathogen of Ralstonia solanacearum - Plant health - Predator-prey interactions - Protists - Rhizosphere - Secondary metabolite genes

    Background: Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators - protists - are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. Results: We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. Conclusions: We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. [MediaObject not available: see fulltext.]

    The ecology of wild zebra finch song – why do they sing?
    Loning, Hugo ; Griffith, Simon C. ; Naguib, M. - \ 2020
    In: Wias Annual Conference 2020 WIAS - p. 35 - 35.
    The zebra finch Taeniopygia guttata is the most studied songbird in the lab but the functions of their song in the wild, Australia’s arid zone, remain unclear. Like many songbirds,male zebra finches sing to attract a female. However, unlike the typically studied songbirds,zebra finches are nomadic birds that live in fission-fusion societies. They pair early in life (sometimes <100 days) and have extremely faithful monogamous relations. Nevertheless,males sing throughout their life. So why do zebra finches sing? In this talk I present data collected at Fowlers Gap Arid Zone Research Station in New South Wales, Australia, home of the world’s only nest box breeding population of zebra finches. Using advanced audio recording techniques and standard behavioural observations, I show that zebra finchessing uncharacteristically soft and that they sing in a variety of contexts, such as in groups at social areas. By studying this lab ‘supermodel’ in the wild, where it evolved, this research may bridge the gap between our understanding of this species in the lab and birdsong in general, already one of the best studied model systems for animal communication.
    Physical activity and risks of breast and colorectal cancer : a Mendelian randomisation analysis
    Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Martin, Richard M. ; Lewis, Sarah J. ; Kazmi, Nabila ; Robinson, Timothy M. ; Albanes, Demetrius ; Aleksandrova, Krasimira ; Berndt, Sonja I. ; Timothy Bishop, D. ; Brenner, Hermann ; Buchanan, Daniel D. ; Bueno-de-Mesquita, Bas ; Campbell, Peter T. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Ellingjord-Dale, Merete ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Giovannucci, Edward ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harlid, Sophia ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hopper, John L. ; Hsu, Li ; María Huerta, José ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Vecchia, Carlo La; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Lindor, Noralane M. ; Lynch, Brigid ; Markowitz, Sanford D. ; Masala, Giovanna ; May, Anne M. ; Milne, Roger ; Monninkhof, Evelyn ; Moreno, Lorena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Perduca, Vittorio ; Pharoah, Paul D.P. ; Platz, Elizabeth A. ; Potter, John D. ; Rennert, Gad ; Riboli, Elio ; Sánchez, Maria Jose ; Schmit, Stephanie L. ; Schoen, Robert E. ; Severi, Gianluca ; Sieri, Sabina ; Slattery, Martha L. ; Song, Mingyang ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Travis, Ruth C. ; Trichopoulou, Antonia ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Vodicka, Pavel ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Peters, Ulrike ; Gunter, Marc J. ; Murphy, Neil - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Physical activity has been associated with lower risks of breast and colorectal cancer in epidemiological studies; however, it is unknown if these associations are causal or confounded. In two-sample Mendelian randomisation analyses, using summary genetic data from the UK Biobank and GWA consortia, we found that a one standard deviation increment in average acceleration was associated with lower risks of breast cancer (odds ratio [OR]: 0.51, 95% confidence interval [CI]: 0.27 to 0.98, P-value = 0.04) and colorectal cancer (OR: 0.66, 95% CI: 0.48 to 0.90, P-value = 0.01). We found similar magnitude inverse associations for estrogen positive (ER+ve) breast cancer and for colon cancer. Our results support a potentially causal relationship between higher physical activity levels and lower risks of breast cancer and colorectal cancer. Based on these data, the promotion of physical activity is probably an effective strategy in the primary prevention of these commonly diagnosed cancers.

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

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

    Revealing the nutrient limitation and cycling for microbes under forest management practices in the Loess Plateau – Ecological stoichiometry
    Zhang, Jiaoyang ; Yang, Xiaomei ; Song, Yahui ; Liu, Hongfei ; Wang, Guoliang ; Xue, Sha ; Liu, Guobin ; Ritsema, Coen J. ; Geissen, Violette - \ 2020
    Geoderma 361 (2020). - ISSN 0016-7061
    Ecological environment - Ecological stoichiometry - Forest management practices - Stoichiometric homeostasis - Threshold elemental ratio

    Forest management practices are commonly used in plantation forestry to obtain renewable energy and harvest biomass, in addition to maintaining the ecological environment, by changing the flow of carbon (C) and nutrients in the food webs of terrestrial ecosystems. To identify which forest management practices, alleviate soil nutrient limitation and impact stoichiometric homeostasis in relation to microbes, we used a Pinus tabuliformis plantation in the Loess Plateau where forest management practices were conducted since 1999. Five forest management practices were implemented: two at the forest level (P. tabuliformis with and without ground litter, CK, LRL) and three of different vegetation restorations after clear-cutting (P. tabuliformis seedlings (SPL), grass land (GL), and shrub land (SL)). Generally, the threshold elemental ratios for carbon:nitrogen (TERC:N; 7.77) and carbon:phosphorus (TERC:P; 44.37) were lower than the ratios influenced by forest management practices. The forest management practices significantly influenced ecoenzymatic activity and the ratios of ecoenzymes; however, the scale of the ecoenzyme activities for acquiring both organic N and organic P to that for acquiring C still follow the global pattern. The regression coefficients of C:N and C:P between the soil and microbial community at 0–20 cm and 20–40 cm depths were also influenced by these practices. Thus, the influence of forest management practices on the soil microbial community was limited by N and P in the Loess Plateau. The soil microbial community changed ecoenzymatic activities and ratios of ecoenzymes and even changed microbial community in order to balance elemental limitations in the soil. Finally, forest management practices have a minimal impact on the stoichiometric homeostasis of the microbial community at our study site.

    Song, Jing ; Xu, Genyan ; Luo, Yongming ; Gao, Hui ; Tang, Wei - \ 2019
    Earth Science Frontiers 26 (2019)6. - ISSN 1005-2321 - p. 192 - 198.
    Bioavailable heavy metals - Criteria for safe utilization of soil - DUMIS - Soil-crop synchronized monitoring - Suitability assessment of soil environmental quality standard

    By compilation of data from field sampling, pot experiment and literature, we evaluated the suitability of the existing national standards (GB 15618-2018 and GB/T 36783-2018) for the classification of soil environmental quality in potato producing areas of Guizhou. The results showed that both soil Cd standards were overly stringent as, for example, these for potatoes grown in mining areas were more likely to exceed food standard. Here, we summarized the inadequacy of the existing sampling methods for soil-crop synchronized monitoring and proposed a sampling theory-based Decision Unit-Multi Increment Sampling method (DUMIS) for soil-crop synchronized monitoring and remediation verification. We proposed that the criteria for safe soil utilization should be derived on a site-specific basis using bioavailable fractions. In order to facilitate the evaluation of soil environmental quality and safety for the agricultural production regions of China, we suggested that further research is needed regarding the use of DUMIS in soil-crop synchronized monitoring and bioavailable fractions based criteria for safe utilization of mild to moderately contaminated soils.

    Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird
    Laine, Veronika N. ; Verhagen, Irene ; Mateman, A.C. ; Pijl, Agata ; Williams, Tony D. ; Gienapp, Phillip ; Oers, Kees van; Visser, Marcel E. - \ 2019
    BMC Genomics 20 (2019). - ISSN 1471-2164
    Aves - Seasonal timing - Selection line - Transcriptomics

    Background: Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding. We studied female great tits (Parus major) from lines artificially selected for early and late timing of breeding that were housed in two contrasting temperature environments in climate-controlled aviaries. We collected hypothalamus, liver and ovary samples at three different time points (before and after onset of egg-laying). For each tissue, we sequenced whole transcriptomes of 12 pools (n = 3 females) to analyse gene expression. Results: Birds from the selection lines differed in expression especially for one gene with clear reproductive functions, zona pellucida glycoprotein 4 (ZP4), which has also been shown to be under selection in these lines. Genes were differentially expressed at different time points in all tissues and most of the differentially expressed genes between the two temperature treatments were found in the liver. We identified a set of hub genes from all the tissues which showed high association to hormonal functions, suggesting that they have a core function in timing of breeding. We also found ample differentially expressed genes with largely unknown functions in birds. Conclusions: We found differentially expressed genes associated with selection line and temperature treatment. Interestingly, the latter mainly in the liver suggesting that temperature effects on egg-laying date may happen down-stream in the physiological pathway. These findings, as well as our datasets, will further the knowledge of the mechanisms of tissue-specific avian seasonality in the future.

    Vessel-length determination using silicone and air injection : Are there artifacts?
    Gao, Hui ; Chen, Ya Jun ; Zhang, Yong Jiang ; Maenpuen, Phisamai ; Lv, Song ; Zhang, Jiao Lin - \ 2019
    Tree Physiology 39 (2019)10. - ISSN 0829-318X - p. 1783 - 1791.
    lianas - maximum vessel length - silicone injection - xylem anatomy

    Xylem vessels are used by most angiosperm plants for long-distance water and nutrient transport. Vessel length is one of the key functional traits determining plant water-transport efficiency. Additionally, determination of maximum vessel length is necessary for correct sample collection and measurements in hydraulic studies to avoid open-vessel and cutting-under-tension artifacts. Air injection and silicone injection (BLUESIL RTV141A and B mixtures) are two widely used methods for maximum vessel length determination. However, the validity of both methods needs to be carefully tested for species with different vessel lengths. In this study, we tested the air-injection and silicone-injection methods using eight species with different vessel lengths: short (<0.5 m), medium (0.5-1 m) and long (>1 m). We employed a novel approach using RTV141A injection without the RTV141B hardener as a reference method because RTV141A cannot penetrate inter-vessel pit membranes and is not prone to hardening/solidification effects during the injection process. The results revealed that the silicone-injection method substantially underestimated the maximum vessel length of all eight species. However, the air-injection method tended to overestimate the maximum vessel length in five out of eight species. The ratio of underestimation of the silicone-injection method was higher for species with longer vessels, but the overestimation of the air-injection method was independent of the vessel length. Moreover, air injection with different pressures - ranging from 40 to 300 kPa - resulted in comparable results. We conclude that the conventional silicone-injection method can underestimate the vessel length, whereas the air-injection method can overestimate the maximum vessel length, particularly for long-vessel led species. We recommend RTV141A-only injection for determining the maximum vessel length, and it can also be used to validate the use of the air-injection and conventional silicone-injection methods for a given species.

    3D camera spots the sick cows
    Song, Xiangyu ; Tol, Rik van der; Bokkers, E.A.M. - \ 2019

    Met een 3D-camera is de conditie van koeten te bepalen, zodat ziekten beter zijn te voorkomen. Promovendus Xiangyu Song ontwierp een methodiek om uiterlijke gezondheidskenmerken van koeien automatisch vast te leggen.

    3D technology helps dairy farmers identify sick cows
    Song, Xiangyu ; Groot Koerkamp, Peter ; Bokkers, E.A.M. ; Tol, Rik van der - \ 2019

    Current precision livestock farming applications for managing dairy cow health are often slow in identifying diseases.

    The skin-deep beauty of dairy cows : Investigation of metabolic disorders by using morphological traits quantified with 3-Dimensional vision
    Song, Xiangyu - \ 2019
    Wageningen University. Promotor(en): P.W.G. Groot Koerkamp, co-promotor(en): E.A.M. Bokkers; P.P.J. van der Tol. - Wageningen : Wageningen University - ISBN 9789463950794 - 121

    Dairy farmers aim to produce high-quality products and meanwhile to ensure the health of their cows. To remain healthy, dairy cows need to eat well. If cows cannot have sufficient food and nutrients to support their daily lives, they could become sick and start changing their physical appearances, such as getting thinner. It is important for farmers to find sick cows as early as possible to offer timely treatment and to prevent further loss. Finding all the sick cows on farms manually based on their physical appearances , however, can cost farmers a great deal of time or money. With the goal of helping farmers, this dissertation has developed an automated system to monitor dairy cows’ physical appearance changes in the whole body and the rumen by using 3D cameras. The automated measurements were compared with expert assessments, and the differences were neglectable. Moreover, the 3D vision system has been applied on a commercial farm to regularly monitor individual cows for a period, where their feeding was changed from silage to fresh grass. Cows responded quickly to this feeding change, and these responses were successfully captured by the 3D vision system. This 3D vision system is automated, non-invasive, and animal-friendly and, hence, it has great potential to be widely used on commercial farms. The automatically measured physical appearances are not only the ‘skin-deep’ beauty of dairy cows but also essential indicators to help farmers in their daily health and feeding management to reach a high-quality production.

    Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice
    Zhao, Fan ; Zhou, Guanghong ; Liu, Xinyue ; Song, Shangxin ; Xu, Xinglian ; Hooiveld, Guido ; Müller, Michael ; Liu, Li ; Kristiansen, Karsten ; Li, Chunbao - \ 2019
    Molecular Nutrition & Food Research 63 (2019)23. - ISSN 1613-4125
    Akkermansia muciniphila - chicken protein - oxidative phosphorylation - soy protein

    Scope: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated. Methods and results: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet. Conclusion: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.

    Cadmium uptake in radish (Raphanus sativus L.) and surficial contaminationimplications for food safety and local soil management: implications for food safety and local soil management
    Xu, Genyan ; Zhang, Sha ; Song, Jing ; Brewer, Roger ; Gao, Hui - \ 2019
    Journal of Soils and Sediments 19 (2019)10. - ISSN 1439-0108 - p. 3585 - 3596.
    Bioavailability - Cd - pH - Potentially toxic metals - Soil criteria - Soil extraction tests

    Purpose: Soil management strategies for agricultural lands contaminated with potentially toxic trace elements, especially cadmium (Cd), are still inadequate and require a precise identification of soils that are not s afe for growing crops. Key soil variables need to be identified to connect soil safety with food safety by reliable models. Materials and methods: Soil variables that affect concentrations of metals in different portions of radish, Raphanus sativus L., were examined as part of a greenhouse experiment. 0.01 M di-sodium-di-hydroxy-ethylenediamine-tretra-acetic acid (Na2H2EDTA) solution was used in a strong rinsing experiment. Cd soil-radish relationships were derived by different modeling approaches and were used to develop local risk screening values for Cd in soil. Results and discussion: The current lab washing procedures readily remove surface Cd adherence but are not adequate to remove surface-deposited lead (Pb), thus overestimating bioaccumulation in plants by mean 111%. Shoot and root tissue Cd concentration in fresh weight basis do not present a significant difference and can be precisely predicted by regression models using different Cd pools and soil pH. Preferably a polynomial surface model can be used in developing local rick screening values that yield concentrations of Cd in radish at or below the Chinese food quality standard of 0.1 mg kg−1 (fresh weight). Conclusions: The bioaccumulation of Cd in radish depends on the Cd bioavailability in soil. But for Pb, surficial particle contamination masks the realistic bioaccumulation. We also demonstrated the usefulness of the polynomial surface model to develop local soil protection guidelines that are helpful to local farmers for proper soil management and avoidance of Cd exceedance in food.

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