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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Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Xing, Yu ; Liu, Yang ; Zhang, Qing ; Nie, Xinghua ; Sun, Yamin ; Zhang, Zhiyong ; Li, Huchen ; Fang, Kefeng ; Wang, Guangpeng ; Huang, Hongwen ; Bisseling, Ton ; Cao, Qingqin ; Qin, Ling - \ 2019
GigaScience 8 (2019)9. - ISSN 2047-217X
Castanea mollissima - annotation - evolution - genome assembly

BACKGROUND: The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima. FINDINGS: We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago. CONCLUSIONS: The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

A lack of complementarity for water acquisition limits yield advantage of oats/vetch intercropping in a semi-arid condition
Zhang, Yue ; Duan, Yu ; Nie, Jiayi ; Yang, Jie ; Ren, Jianhong ; Werf, Wopke van der; Evers, Jochem B. ; Zhang, Jun ; Su, Zhicheng ; Zhang, Lizhen - \ 2019
Agricultural Water Management 225 (2019). - ISSN 0378-3774
Daily water use - Land equivalent ratio - Productivity - Water equivalent ratio - Water use efficiency

Oats (Avena sativa L.) and hairy vetch (Vicia villosa) are well adapted crop species for production in semi-arid environments, such as in Inner Mongolia, China, where due to variable rainfall, farmers do not apply fertilizer. We hypothesized that the use of a mixture of a cereal and a legume could enhance yields under these low input conditions, because integrating an N-fixing legume in the system could mitigate N limitation for the cereal and enhance its growth. A nine-year (2008–2016) field experiment was set up with three treatments: sole oats, sole vetch and oats/vetch strip intercropping. These cropping systems were grown continuously in the same plots, to allow accrual of long-term effects. Yields and water use were quantified in years 7–9 of the experiment (2014 to 2016). With a 50/50 ratio of the area sown to the two species, the intercropped oats had a relative yield of 0.59 and intercropped vetch had a relative yield of 0.45. Oats was the dominant crop characterized by a relative yield per plant of 1.18, compared to a relative yield per plant of vetch of 0.89. However, the land equivalent ratio (LER), expressing the comparative efficiency of land use in intercropping, and the water equivalent ratio (WER), the comparative system level water use efficiency of the intercrop relative to sole crops, were both not significantly different from one. Thus we reject the hypothesis that oat/vetch intercropping increases land productivity and water use efficiency. From differences in results in years with more rainfall and years with less rainfall, we infer that yields of both species are mostly limited by water availability. On average over the three years, the yield disadvantage of vetch was fully compensated by the yield advantage of oats, due to a lack of complementarity for water acquisition. This conclusion can be generalized to the testable prediction that species selection for productive intercropping should focus on achieving complementarity for traits that interact with the factor most constraining productivity, which was rainfall in this particular crop system under the conditions of the study.

The future of intercropping under growing resource scarcity and declining grain prices - A model analysis based on a case study in Northwest China
Hong, Yu ; Berentsen, Paul ; Heerink, Nico ; Shi, Minjun ; Werf, Wopke van der - \ 2019
Agricultural Systems 176 (2019). - ISSN 0308-521X
China - Intercropping - Labor - Maize price - Water

Intercropping, i.e. mixed crop species cultivation on a field, can potentially reduce pressure on land and water resources by generating higher resource use efficiencies and crop yields through exploitation of complementarities between species. Intercropping systems in China and elsewhere have come under pressure through labor migration, growing water scarcity, changing crop prices and other factors. However, little hard evidence is available on how these socio-economic factors interplay and affect the prevalence of intercropping systems now and in the near future. The objective of this study is to explore the effect of growing scarcity of (water and labor) resources and declining (maize) grain prices on the share of intercropping in the optimal cropping plan and on associated agricultural income levels in an intercropping-dominated agricultural system in China. To undertake this analysis, we developed a mathematical programming model to simulate crop production for a model village in Gaotai county in the Hexi Corridor in northwest China, for given resources and economic conditions in 2013 and possible changes (scenarios) in the future. In the Hexi Corridor, conventional wheat/maize intercropping contributed greatly to rising food production while cash crops integrated with maize provided important cash income. With the introduction of seed crops and stricter water regulations, intercropping has become less prevalent in this area in recent years. In the absence of water constraints and at price levels and labor availability in 2013, our model results indicate that an optimal land use would entail that all land would be devoted to intercropping. Sole cumin and sole cotton enter the optimal cropping plan when water becomes scarce and the maize price declines substantially, while increases in hired labor wages have a strong negative impact on intercropping only when on-farm labor becomes scarce.

Excreta emissions in progeny of low and high enteric methane yield selection line sheep fed pasture of different qualities
Jonker, A. ; MacLean, S. ; Woyimo Woju, C. ; Garcia Rendon Calzada, M. ; Yu, W. ; Molano, G. ; Hickey, S. ; Pinares-Patiño, C.S. ; McEwan, J.C. ; Janssen, P.H. ; Sandoval, E. ; Lewis, S. ; Rowe, S. - \ 2019
Animal Feed Science and Technology 257 (2019). - ISSN 0377-8401
Animal variation - Breeding value - Greenhouse gas - Nitrous oxide - Repeatability - Urine

Selection of sheep with low enteric methane (CH4) emissions is a greenhouse gas (GHG) mitigation option suitable for pastoral systems. However, the effect of breeding sheep with low enteric CH4 emissions on excreta output and associated CH4 and nitrous oxide (N2O) emissions and therefore total GHG emissions are not known. The objective of the current experiments were to determine excreta output, and estimate associated GHG emissions, from progeny of low and high enteric CH4 per unit of dry matter intake (DMI) selection line sheep (CH4/DMI). The animals were fed two qualities of cut perennial ryegrass-based pasture (very mature vs. vegetative, 12 animals per CH4/DMI line) in Exp. 1 and cut pasture in two repeated seasons (autumn and winter; 15 animals per CH4/DMI line × 2 seasons) in Exp. 2. Total faecal and urine output was determined on individual animals, followed by enteric CH4 emission measurements in respiration chambers. GHG emissions from urine (N2O) and faeces (CH4 and N2O) were estimated based on New Zealand Agricultural GHG Inventory methodology. There was no interaction between CH4/DMI selection line and diet quality in Exp. 1 or seasons in Exp.2. Total daily faecal output of DM, organic matter (OM) and neutral detergent fibre (NDF; all g/d) and associated calculated faecal CH4 emissions were greater for low compared to high CH4/DMI sheep in Exp. 1 (P < 0.05), while being similar between CH4/DMI selection lines in Exp. 2. Nitrogen (N) excretion and N partitioning into urine, faeces and body retention, and calculated excreta N emissions, were mostly similar between CH4/DMI selection line sheep in both experiments. Except, faecal N output (g/d and per unit of N intake) and associated calculated direct faecal N2O-N emissions (g/d) were greater in low compared to high CH4/DMI sheep in Exp. 1 (P < 0.05). Enteric CH4 emissions were numerically 8% less (P = 0.15) in Exp.1 and 10% less (P = 0.004) in Exp. 2 and total animal level GHG emissions (CH4 and N2O) were numerically 7% less (P = 0.21) in Exp. 1 and 8% less (P = 0.006) in Exp.2 for progeny of the low compared to the high CH4/DMI line sheep. In conclusion, the magnitude of difference in enteric CH4 (expressed as CO2-equivalent) between low and high CH4/DMI selection line sheep were still present when CH4 from faeces and N2O emissions from urine and faeces were also accounted for. The animal genetic traits were expressed independent of environmental factors, i.e. pasture quality and season.

Long-chain vitamin K2 production in Lactococcus lactis is influenced by temperature, carbon source, aeration and mode of energy metabolism
Liu, Yue ; Bennekom, Eric O. Van; Zhang, Yu ; Abee, Tjakko ; Smid, Eddy J. - \ 2019
Microbial Cell Factories 18 (2019)1. - ISSN 1475-2859
Aeration - Carbon source - Long-chain MKs - Menaquinone - Natural enrichment - Respiration - Vitamin K2

Background: Vitamin K2 (menaquinone, MK-n) is a lipid-soluble vitamin that functions as a carboxylase co-factor for maturation of proteins involved in many vital physiological processes in humans. Notably, long-chain vitamin K2 is produced by bacteria, including some species and strains belonging to the group of lactic acid bacteria (LAB) that play important roles in food fermentation processes. This study was performed to gain insights into the natural long-chain vitamin K2 production capacity of LAB and the factors influencing vitamin K2 production during cultivation, providing a basis for biotechnological production of vitamin K2 and in situ fortification of this vitamin in food products. Results: We observed that six selected Lactococcus lactis strains produced MK-5 to MK-10, with MK-8 and MK-9 as the major MK variant. Significant diversities between strains were observed in terms of specific concentrations and titres of vitamin K2. L. lactis ssp. cremoris MG1363 was selected for more detailed studies of the impact of selected carbon sources tested under different growth conditions [i.e. static fermentation (oxygen absent, heme absent); aerobic fermentation (oxygen present, heme absent) and aerobic respiration (oxygen present, heme present)] on vitamin K2 production in M17 media. Aerobic fermentation with fructose as a carbon source resulted in the highest specific concentration of vitamin K2: 3.7-fold increase compared to static fermentation with glucose, whereas aerobic respiration with trehalose resulted in the highest titre: 5.2-fold increase compared to static fermentation with glucose. When the same strain was applied to quark fermentation, we consistently observed that altered carbon source (fructose) and aerobic cultivation of the pre-culture resulted in efficient vitamin K2 fortification in the quark product. Conclusions: With this study we demonstrate that certain LAB strains can be employed for efficient production of long-chain vitamin K2. Strain selection and optimisation of growth conditions offer a viable strategy towards natural vitamin K2 enrichment of fermented foods, and to improved biotechnological vitamin K2 production processes.

Towards on-site visual detection of proteases in food matrices
Klisara, Nevena ; Yu, You Mei ; Palaniappan, Alagappan ; Liedberg, Bo - \ 2019
Analytica Chimica Acta 1078 (2019). - ISSN 0003-2670 - p. 182 - 188.
Food safety - Magnetic beads - Peptide - Proteases - Visual detection

Early detection of toxic proteases in food matrices plays a major role in preventing the occurrence of diseases as well as outbreaks. However, on-site detection of proteases, for instance, botulinum, anthrax and cholera in food matrices remains challenging due to their extremely low lethal dose levels. Here, we report a lateral flow assay (LFA) in a dipstick format for on-site visual detection of proteases in food matrices. The light chain of BoNT serotype A (BoNT/A LC) is used as a model system for validation of the proposed assay using magnetic beads conjugated to a synthetic peptide that provide a specific cleavage site for BoNT/A LC. Magnetic beads serve as both reporters for visual detection and as facilitators for sample clean-up, owing to the efficient magnetic separation protocol adopted. Digestion of the peptide substrate by BoNT/A LC for 5 h followed by the dipstick assay yields a reduction in color intensity of the test line on the dipstick compared to the control line obtained using an un-cleaved peptide substrate. Concentration dependent responses for the assay in carrot juice were obtained with a limit of detection (LOD) of 1 nM/2.5 nM (with/without amplification), also supported by RGB (ΔE) analysis, indicating the potential of the proposed methodology for on-site assaying of proteases in food matrices. Unlike typical affinity-based assays that yield a collective response for the active and inactive forms of the proteases, the proposed functional LFA targets only the active form, thereby enabling a more precise analysis for preventing potential false-positives. The proposed approach could be extended for detection of BoNT serotypes and other proteases in food matrices, upon utilizing appropriate substrates with specific cleavage sites.

Toward the improvement of total nitrogen deposition budgets in the United States
Walker, J.T. ; Beachley, G. ; Amos, H.M. ; Baron, J.S. ; Bash, J. ; Baumgardner, R. ; Bell, M.D. ; Benedict, K.B. ; Chen, X. ; Clow, D.W. ; Cole, A. ; Coughlin, J.G. ; Cruz, K. ; Daly, R.W. ; Decina, S.M. ; Elliott, E.M. ; Fenn, M.E. ; Ganzeveld, L. ; Gebhart, K. ; Isil, S.S. ; Kerschner, B.M. ; Larson, R.S. ; Lavery, T. ; Lear, G.G. ; Macy, T. ; Mast, M.A. ; Mishoe, K. ; Morris, K.H. ; Padgett, P.E. ; Pouyat, R.V. ; Puchalski, M. ; Pye, H.O.T. ; Rea, A.W. ; Rhodes, M.F. ; Rogers, C.M. ; Saylor, R. ; Scheffe, R. ; Schichtel, B.A. ; Schwede, D.B. ; Sexstone, G.A. ; Sive, B.C. ; Sosa, R. ; Templer, P.H. ; Thompson, T. ; Tong, D. ; Wetherbee, G.A. ; Whitlow, T.H. ; Wu, Z. ; Yu, Z. ; Zhang, L. - \ 2019
Science of the Total Environment 691 (2019). - ISSN 0048-9697 - p. 1328 - 1352.
Ammonia - Dry deposition - Organic nitrogen - Oxidized nitrogen - Reactive nitrogen - Wet deposition

Frameworks for limiting ecosystem exposure to excess nutrients and acidity require accurate and complete deposition budgets of reactive nitrogen (Nr). While much progress has been made in developing total Nr deposition budgets for the U.S., current budgets remain limited by key data and knowledge gaps. Analysis of National Atmospheric Deposition Program Total Deposition (NADP/TDep) data illustrates several aspects of current Nr deposition that motivate additional research. Averaged across the continental U.S., dry deposition contributes slightly more (55%) to total deposition than wet deposition and is the dominant process (>90%) over broad areas of the Southwest and other arid regions of the West. Lack of dry deposition measurements imposes a reliance on models, resulting in a much higher degree of uncertainty relative to wet deposition which is routinely measured. As nitrogen oxide (NOx) emissions continue to decline, reduced forms of inorganic nitrogen (NHx = NH3 + NH4 +) now contribute >50% of total Nr deposition over large areas of the U.S. Expanded monitoring and additional process-level research are needed to better understand NHx deposition, its contribution to total Nr deposition budgets, and the processes by which reduced N deposits to ecosystems. Urban and suburban areas are hotspots where routine monitoring of oxidized and reduced Nr deposition is needed. Finally, deposition budgets have incomplete information about the speciation of atmospheric nitrogen; monitoring networks do not capture important forms of Nr such as organic nitrogen. Building on these themes, we detail the state of the science of Nr deposition budgets in the U.S. and highlight research priorities to improve deposition budgets in terms of monitoring and flux measurements, leaf- to regional-scale modeling, source apportionment, and characterization of deposition trends and patterns.

Evaluation of the performance of existing mathematical models predicting enteric methane emissions from ruminants: Animal categories and dietary mitigation strategies
Benaouda, Mohammed ; Martin, Cécile ; Li, Xinran ; Kebreab, Ermias ; Hristov, Alexander N. ; Yu, Zhongtang ; Yáñez-Ruiz, David R. ; Reynolds, Christopher K. ; Crompton, L.A. ; Dijkstra, Jan ; Bannink, André ; Schwarm, Angela ; Kreuzer, Michael ; McGee, Mark ; Lund, P. ; Hellwing, Anne L.F. ; Weisbjerg, Martin R. ; Moate, Peter J. ; Bayat, A.R. ; Shingfield, Kevin J. ; Peiren, Nico ; Eugène, M. - \ 2019
Animal Feed Science and Technology 255 (2019). - ISSN 0377-8401
Dietary strategy - Methane emission - Model evaluation - Ruminant

The objective of this study was to evaluate the performance of existing models predicting enteric methane (CH4) emissions, using a large database (3183 individual data from 103 in vivo studies on dairy and beef cattle, sheep and goats fed diets from different countries). The impacts of dietary strategies to reduce CH4 emissions, and of diet quality (described by organic matter digestibility (dOM) and neutral-detergent fiber digestibility (dNDF)) on model performance were assessed by animal category. The models were first assessed based on the root mean square prediction error (RMSPE) to standard deviation of observed values ratio (RSR) to account for differences in data between models and then on the RMSPE. For dairy cattle, the CH4 (g/d) predicting model based on feeding level (dry matter intake (DMI)/body weight (BW)), energy digestibility (dGE) and ether extract (EE) had the smallest RSR (0.66) for all diets, as well as for the high-EE diets (RSR = 0.73). For mitigation strategies based on lowering NDF or improving dOM, the same model (RSR = 0.48 to 0.60) and the model using DMI and neutral- and acid-detergent fiber intakes (RSR = 0.53) had the smallest RSR, respectively. For diets with high starch (STA), the model based on nitrogen, ADF and STA intake presented the smallest RSR (0.84). For beef cattle, all evaluated models performed moderately compared with the models of dairy cattle. The smallest RSR (0.83) was obtained using variables of energy intake, BW, forage content and dietary fat, and also for the high-EE and the low-NDF diets (RSR = 0.84 to 0.86). The IPCC Tier 2 models performed better when dietary STA, dOM or dNDF were high. For sheep and goats, the smallest RSR was observed from a model for sheep based on dGE intake (RSR = 0.61). Both IPCC models had low predictive ability when dietary EE, NDF, dOM and dNDF varied (RSR = 0.57 to 1.31 in dairy, and 0.65 to 1.24 in beef cattle). The performance of models depends mostly on explanatory variables and not on the type of data (individual vs. treatment means) used in their development or evaluation. Some empirical models give satisfactory prediction error compared with the error associated with measurement methods. For better prediction, models should include feed intake, digestibility and additional information on dietary concentrations of EE and structural and nonstructural carbohydrates to account for different dietary mitigating strategies.

Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Prediction of enteric methane production, yield and intensity of beef cattle using an intercontinental database
Lingen, Henk J. van; Niu, Mutian ; Kebreab, Ermias ; Valadares Filho, Sebastião C. ; Rooke, John A. ; Duthie, Carol Anne ; Schwarm, Angela ; Kreuzer, Michael ; Hynd, Phil I. ; Caetano, Mariana ; Eugène, Maguy ; Martin, Cécile ; McGee, Mark ; O'Kiely, Padraig ; Hünerberg, Martin ; McAllister, Tim A. ; Berchielli, Telma T. ; Messana, Juliana D. ; Peiren, Nico ; Chaves, Alex V. ; Charmley, Ed ; Cole, N.A. ; Hales, Kristin E. ; Lee, Sang Suk ; Berndt, Alexandre ; Reynolds, Christopher K. ; Crompton, Les A. ; Bayat, Ali R. ; Yáñez-Ruiz, David R. ; Yu, Zhongtang ; Bannink, André ; Dijkstra, Jan ; Casper, David P. ; Hristov, Alexander N. - \ 2019
Agriculture, Ecosystems and Environment 283 (2019). - ISSN 0167-8809
Dietary variables - Empirical modeling - Forage content - Geographical region - Methane emission

Enteric methane (CH4) production attributable to beef cattle contributes to global greenhouse gas emissions. Reliably estimating this contribution requires extensive CH4 emission data from beef cattle under different management conditions worldwide. The objectives were to: 1) predict CH4 production (g d−1 animal−1), yield [g (kg dry matter intake; DMI)−1] and intensity [g (kg average daily gain)−1] using an intercontinental database (data from Europe, North America, Brazil, Australia and South Korea); 2) assess the impact of geographic region, and of higher- and lower-forage diets. Linear models were developed by incrementally adding covariates. A K-fold cross-validation indicated that a CH4 production equation using only DMI that was fitted to all available data had a root mean square prediction error (RMSPE; % of observed mean) of 31.2%. Subsets containing data with ≥25% and ≤18% dietary forage contents had an RMSPE of 30.8 and 34.2%, with the all-data CH4 production equation, whereas these errors decreased to 29.3 and 28.4%, respectively, when using CH4 prediction equations fitted to these subsets. The RMSPE of the ≥25% forage subset further decreased to 24.7% when using multiple regression. Europe- and North America-specific subsets predicted by the best performing ≥25% forage multiple regression equation had RMSPE of 24.5 and 20.4%, whereas these errors were 24.5 and 20.0% with region-specific equations, respectively. The developed equations had less RMSPE than extant equations evaluated for all data (22.5 vs. 23.2%), for higher-forage (21.2 vs. 23.1%), but not for the lower-forage subsets (28.4 vs. 27.9%). Splitting the dataset by forage content did not improve CH4 yield or intensity predictions. Predicting beef cattle CH4 production using energy conversion factors, as applied by the Intergovernmental Panel on Climate Change, indicated that adequate forage content-based and region-specific energy conversion factors improve prediction accuracy and are preferred in national or global inventories.

Invited review: Nitrogen in ruminant nutrition: A review of measurement techniques
Hristov, A.N. ; Bannink, A. ; Crompton, L.A. ; Huhtanen, P. ; Kreuzer, M. ; McGee, M. ; Nozière, P. ; Reynolds, C.K. ; Bayat, A.R. ; Yáñez-Ruiz, D.R. ; Dijkstra, J. ; Kebreab, E. ; Schwarm, A. ; Shingfield, K.J. ; Yu, Z. - \ 2019
Journal of Dairy Science 102 (2019)7. - ISSN 0022-0302 - p. 5811 - 5852.
environment - manure - metabolism - nitrogen - ruminant animal - technique

Nitrogen is a component of essential nutrients critical for the productivity of ruminants. If excreted in excess, N is also an important environmental pollutant contributing to acid deposition, eutrophication, human respiratory problems, and climate change. The complex microbial metabolic activity in the rumen and the effect on subsequent processes in the intestines and body tissues make the study of N metabolism in ruminants challenging compared with nonruminants. Therefore, using accurate and precise measurement techniques is imperative for obtaining reliable experimental results on N utilization by ruminants and evaluating the environmental impacts of N emission mitigation techniques. Changeover design experiments are as suitable as continuous ones for studying protein metabolism in ruminant animals, except when changes in body weight or carryover effects due to treatment are expected. Adaptation following a dietary change should be allowed for at least 2 (preferably 3) wk, and extended adaptation periods may be required if body pools can temporarily supply the nutrients studied. Dietary protein degradability in the rumen and intestines are feed characteristics determining the primary AA available to the host animal. They can be estimated using in situ, in vitro, or in vivo techniques with each having inherent advantages and disadvantages. Accurate, precise, and inexpensive laboratory assays for feed protein availability are still needed. Techniques used for direct determination of rumen microbial protein synthesis are laborious and expensive, and data variability can be unacceptably large; indirect approaches have not shown the level of accuracy required for widespread adoption. Techniques for studying postruminal digestion and absorption of nitrogenous compounds, urea recycling, and mammary AA metabolism are also laborious, expensive (especially the methods that use isotopes), and results can be variable, especially the methods based on measurements of digesta or blood flow. Volatile loss of N from feces and particularly urine can be substantial during collection, processing, and analysis of excreta, compromising the accuracy of measurements of total-tract N digestion and body N balance. In studying ruminant N metabolism, nutritionists should consider the longer term fate of manure N as well. Various techniques used to determine the effects of animal nutrition on total N, ammonia- or nitrous oxide-emitting potentials, as well as plant fertilizer value, of manure are available. Overall, methods to study ruminant N metabolism have been developed over 150 yr of animal nutrition research, but many of them are laborious and impractical for application on a large number of animals. The increasing environmental concerns associated with livestock production systems necessitate more accurate and reliable methods to determine manure N emissions in the context of feed composition and ruminant N metabolism.

Inter-provincial electricity transmissions’ co-benefit of national water savings in China
Liao, Xiawei ; Chai, Li ; Jiang, Yu ; Ji, Junping ; Zhao, Xu - \ 2019
Journal of Cleaner Production 229 (2019). - ISSN 0959-6526 - p. 350 - 357.
Co-benefit - Electricity transmission - Water conservation - Water-energy nexus

Interprovincial electricity transmissions have been utilised in China to overcome the country's imbalanced social-economic development and resource endowments. A bottom-up technology-based model is adopted to estimate water uses in electricity-exporting provinces to produce the transmitted electricity as well as opportunistic water savings in the receiving provinces. The results highlight that, in 2014, on a national scale, electricity transmissions generated co-benefit of saving 20.1 billion m³ of water nationally due to the electric power sector's water productivity differences in the exporting and importing provinces. Taking regional water stresses into account, 10.98 billion m³ of national scarce water saving is realized through electricity transmissions. Moreover, electricity transmissions by China's proposed 12 future transmission lines are expected to use additional 3.22 billion m³ of water in the electricity-exporting provinces. As more water-intensive technologies, e.g. open-loop cooling, are more commonly utilised in the electricity-receiving provinces, a total amount of 16.97 billion m³ of water use will be avoided nationally. Water-use efficiency for power production should be improved in all regions. Transmitted power imports should still be encouraged in water-scarce regions to alleviate their water stresses while power exports should be shifted away from water-stressed regions to water-abundant ones. Energy transformation by utilising gas-fired capacity and hydropower in water-abundant Southern China could be advanced.

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.

Airborne host–plant manipulation by whiteflies via an inducible blend of plant volatiles
Zhang, Peng Jun ; Wei, Jia Ning ; Zhao, Chan ; Zhang, Ya Fen ; Li, Chuan You ; Liu, Shu Sheng ; Dicke, Marcel ; Yu, Xiao Ping ; Turlings, Ted C.J. - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)15. - ISSN 0027-8424 - p. 7387 - 7396.
Herbivore-induced plant volatiles - Jasmonic acid - Salicylic acid - Tomato - Whiteflies

The whitefly Bemisia tabaci is one of the world’s most important invasive crop pests, possibly because it manipulates plant defense signaling. Upon infestation by whiteflies, plants mobilize salicylic acid (SA)-dependent defenses, which mainly target pathogens. In contrast, jasmonic acid (JA)-dependent defenses are gradually suppressed in whitefly-infested plants. The down-regulation of JA defenses make plants more susceptible to insects, including whiteflies. Here, we report that this host–plant manipulation extends to neighboring plants via airborne signals. Plants respond to insect attack with the release of a blend of inducible volatiles. Perception of these volatiles by neighboring plants usually primes them to prepare for an imminent attack. Here, however, we show that whitefly-induced tomato plant volatiles prime SA-dependent defenses and suppress JA-dependent defenses, thus rendering neighboring tomato plants more susceptible to whiteflies. Experiments with volatiles from caterpillar-damaged and pathogen-infected plants, as well as with synthetic volatiles, confirm that whiteflies modify the quality of neighboring plants for their offspring via whitefly-inducible plant volatiles.

Intercropping cereals with faba bean reduces plant disease incidence regardless of fertilizer input; a meta-analysis
Zhang, Chaochun ; Dong, Yan ; Tang, Li ; Zheng, Yi ; Makowski, David ; Yu, Yang ; Zhang, Fusuo ; Werf, Wopke van der - \ 2019
European Journal of Plant Pathology 154 (2019)4. - ISSN 0929-1873 - p. 931 - 942.
Disease control - Intercropping - Meta-analysis - Nutrient management

Ecological intensification of agriculture calls for ecological mechanisms to replace anthropogenic inputs. Cereal/legume intercropping increases yields due to species complementarities, it produces high protein food and feed, and it reduces the need for artificial N fertilizer because legumes fix N biologically. In addition, intercropping has the potential to suppress plant diseases, but its efficacy for disease suppression in cereal/legume mixtures has not been well characterized quantitatively. Here we conducted meta-analysis to quantify the disease suppressive effect of intercropping cereals with legumes at different levels of N fertilizer. Intercropping reduced disease incidence (measured by the odds ratio of disease occurrence) by 45% on average. This reduction was significant (P < 0.01) for four out of six studied pathogens: yellow rust (Puccinia striiformis f.sp. tritici) and mildew (Blumeria graminis) in wheat (Triticum aestivum), and chocolate spot (Botrytis fabae) and Fusarium wilt (Fusarium oxysporum) in faba bean (Vicia faba). Disease reduction was marginally significant for yellow rust in barley (Puccinia striiformis f.sp. hordei) (P < 0.10) and not significant for bean rust (Uromyces fabae). The reduction in disease incidence was greatest during the early stages of epidemics. N fertilizer strongly increased the incidence of powdery mildew of wheat, but it did not affect the incidence of the other diseases and it did not affect the effectiveness of intercropping as a management strategy for disease control. While nitrogen input increased powdery mildew incidence in both sole and intercropped wheat, the incidence was lower in the intercropped than sole wheat at all levels of N input. The disease suppressive effect of intercropping on wheat powdery mildew or any other disease was not affected by the amount of nitrogen fertilizer. The results show that intercropping has a substantial and consistent effect on disease incidence in cereal/faba bean mixtures across studies, but is not sufficient to provide complete disease control. Intercropping is therefore best used as a component in an integrated approach for managing plant diseases.

Intercropping contributes to a higher technical efficiency in smallholder farming : Evidence from a case study in Gaotai County, China
Hong, Yu ; Heerink, Nico ; Zhao, Minjuan ; Werf, Wopke van der - \ 2019
Agricultural Systems 173 (2019). - ISSN 0308-521X - p. 317 - 324.
China - Intercropping - Resource-use efficiency - Stochastic production frontier - Technical efficiency

Intercropping entails the concurrent production of two or more crop species in the same field. This traditional farming method generally results in a highly efficient use of land, but whether it also contributes to a higher technical efficiency remains unclear. Technical efficiency refers to the efficiency with which a given set of natural resources and other inputs can be used to produce crops. In this study, we examined the contribution of maize-based relay-strip intercropping to the technical efficiency of smallholder farming in northwest China. Data on the inputs and crop production of 231 farms were collected for the 2013 agricultural season using a farm survey held in Gaotai County, Gansu Province, China. Controlling for other factors, we found that the technical efficiency scores of these farms were positively affected by the proportion of land assigned to intercropping. This finding indicates that the potential negative effects of intercropping on the use efficiency of labour and other resources are more than offset by its higher land-use efficiency when compared with monocropping.

Disentangling the genetics of lean mass
Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

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.

Erratum to: dissolved organic carbon in permafrost regions: a review
Ma, Qiang ; Jin, Huijun ; Yu, Congrong ; Bense, Victor F. - \ 2019
Science China Earth Sciences 62 (2019)4. - ISSN 1674-7313 - p. 750 - 750.

The article Dissolved organic carbon in permafrost regions: A review, written by Qiang MA, Huijun JIN, Congrong YU, and Victor F. BENSE, was erroneously originally published online without open access. After publication in Vol 62 Issue 2 this was corrected and the article is now an open access publication. Therefore, the copyright of the article has been changed to

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)4. - ISSN 0340-6717 - p. 307 - 326.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
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