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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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 (2019). - ISSN 0340-6717 - 20 p.
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.
Dystrophin is required for normal synaptic gain in the Drosophila olfactory circuit
Jantrapirom, Salinee ; Cao, De Shou ; Wang, Jing W. ; Hing, Huey ; Tabone, Christopher J. ; Lantz, Kathryn ; Belle, J.S. de; Qiu, Yu Tong ; Smid, Hans M. ; Yamaguchi, Masamitsu ; Fradkin, Lee G. ; Noordermeer, Jasprina N. ; Potikanond, Saranyapin - \ 2019
Brain Research 1712 (2019). - ISSN 0006-8993 - p. 158 - 166.
Antennal lobe - Behavior - Drosophila melanogaster - Dystrophin - Olfaction - Olfactory receptor neurons - Projection neurons

The Drosophila olfactory system provides an excellent model to elucidate the neural circuits that control behaviors elicited by environmental stimuli. Despite significant progress in defining olfactory circuit components and their connectivity, little is known about the mechanisms that transfer the information from the primary antennal olfactory receptor neurons to the higher order brain centers. Here, we show that the Dystrophin Dp186 isoform is required in the olfactory system circuit for olfactory functions. Using two-photon calcium imaging, we found the reduction of calcium influx in olfactory receptor neurons (ORNs) and also the defect of GABA A mediated inhibitory input in the projection neurons (PNs) in Dp186 mutation. Moreover, the Dp186 mutant flies which display a decreased odor avoidance behavior were rescued by Dp186 restoration in the Drosophila olfactory neurons in either the presynaptic ORNs or the postsynaptic PNs. Therefore, these results revealed a role for Dystrophin, Dp 186 isoform in gain control of the olfactory synapse via the modulation of excitatory and inhibitory synaptic inputs to olfactory projection neurons.

Dissolved organic carbon in permafrost regions : A review
Ma, Qiang ; Jin, Huijun ; Yu, Congrong ; Bense, Victor F. - \ 2019
Science China Earth Sciences 62 (2019)2. - ISSN 1674-7313 - p. 349 - 364.
Aquatic ecosystem - Carbon biodegradability - Dissolved organic carbon (DOC) - DOC export - Permafrost degradation

A large quantity of organic carbon (C) is stored in northern and elevational permafrost regions. A portion of this large terrestrial organic C pool will be transferred by water into soil solution (~0.4 Pg C yr−1) (1 Pg=1015 g), rivers (~0.06 Pg C yr−1), wetlands, lakes, and oceans. The lateral transport of dissolved organic carbon (DOC) is the primary pathway, impacting river biogeochemistry and ecosystems. However, climate warming will substantially alter the lateral C shifts in permafrost regions. Vegetation, permafrost, precipitation, soil humidity and temperature, and microbial activities, among many other environmental factors, will shift substantially under a warming climate. It remains uncertain as to what extent the lateral C cycle is responding, and will respond, to climate change. This paper reviews recent studies on terrestrial origins of DOC, biodegradability, transfer pathways, and modelling, and on how to forecast of DOC fluxes in permafrost regions under a warming climate, as well as the potential anthropogenic impacts on DOC in permafrost regions. It is concluded that: (1) surface organic layer, permafrost soils, and vegetation leachates are the main DOC sources, with about 4.72 Pg C DOC stored in the topsoil at depths of 0–1 m in permafrost regions; (2) in-stream DOC concentrations vary spatially and temporally to a relatively small extent (1–60 mg C L−1) and annual export varies from 0.1–10 g C m–2 yr–1; (3) biodegradability of DOC from the thawing permafrost can be as high as 71%, with a median at 52%; (4) DOC flux is controlled by multiple factors, mainly including vegetation, soil properties, permafrost occurrence, river discharge and other related environmental factors, and (5) many statistical and process-based models have been developed, but model predictions are inconsistent with observational results largely dependent on the individual watershed characteristics and future discharge trends. Thus, it is still difficult to predict how future lateral C flux will respond to climate change, but changes in the DOC regimes in individual catchments can be predicted with a reasonable reliability. It is advised that sampling protocols and preservation and analysis methods should be standardized, and analytical techniques at molecular scales and numerical modeling on thermokarsting processes should be prioritized.

Leaching of microplastics by preferential flow in earthworm (Lumbricus terrestris) burrows
Yu, Miao ; Ploeg, Martine Van Der; Lwanga, Esperanza Huerta ; Yang, Xiaomei ; Zhang, Shaoliang ; Ma, Xiaoyi ; Ritsema, Coen J. ; Geissen, Violette - \ 2019
Environmental Chemistry 16 (2019)1. - ISSN 1448-2517 - p. 31 - 40.
floating method - groundwater - litter - soil column

In the current study, we examine how the activities of earthworms (Lumbricus terrestris) affect microplastic (MP) distribution and concentration in soil, with a focus on low density polyethylene (LDPE). We also want to determine if MPs can be flushed out with water. We used a laboratory sandy soil column (polyvinyl chloride tube) experimental set-up and tested five different treatments: (1) treatment with just soil (control) to check if the saturated conductivity (Ksat) could be impacted by MP, (2) treatment with MP, (3) treatment with MP and litter, (4) treatment with earthworms and litter as a second control for treatment 5 and (5) treatment with MPs, earthworms and litter. Each treatment consisted of eight replicates. For the treatments with MP, the concentration of MP added at the start of the experiment was 7 % by weight (3.97 g, polyethylene, 50 % 1 mm-250 μm, 30 % 250 μm-150 μm and 20 % <150 μm) based on 52.78 g of dry litter from Populus nigra. In the treatments using earthworms, two adult earthworms, with an initial average weight of (7.14 ± 0.26) g, were placed in each column. Results showed that LDPE particles could be introduced into the soil by the earthworms. MP particles were detected in each soil sample and within different soil layers for the earthworm treatments. Earthworms showed a tendency to transport the smaller MP particles and that the amount of MPs in size class <250 μm increased in soil samples with increasing soil depth in comparison to the other size classes. After leaching, MPs were only detected in the leachate from the treatments with the earthworms, and the MP had similar size distributions as the soil samples in the 40-50 cm layer of the treatment with MP, earthworms and litter. The results of this study clearly show that biogenic activities can mobilise MP transport from the surface into the soil and even be leached into drainage. It is highly likely that biogenic activities constitute a potential pathway for MPs to be transported into soil and groundwater.

Ionic interaction and liquid absorption by wood in lignocellulose inorganic mineral binder composites
Doudart de la Grée, G.C.H. ; Caprai, V. ; Dam, J.E.G. van; As, H. van; Brouwers, H.J.H. ; Yu, Q.L. - \ 2019
Journal of Cleaner Production 206 (2019). - ISSN 0959-6526 - p. 808 - 818.
Alkali activated binder - Ionic behaviour - Lignocellulose - Moisture content - NMR - Reaction kinetics

This study investigates the suitability of alkali activated binders to replace Portland cement for lignocellulosic mineral-binder composite, aiming to lower the CO2 footprint. The effects of wood composition on the reaction kinetics of the binders and the formation of the reaction products are studied using isothermal calorimetry and ion chromatography. The ionic behaviour analysis of Ca2+ and Na+ ions in the binders shows that in presence of wood, a neutralisation of OH ions and reduction of Ca2+ and Na+ ions during the first 24 h of curing take place, which alters the formation of C-A-S-H and N-A-S-H gels and influences the final composite performance. Moreover, the position of water absorbed by wood with different moisture levels is investigated by using T2 relaxometry Time Domain (TD) NMR to understand the required water amount for the binder reaction as well as the liquid uptake of the wood and occurring ion migration. The results show that a hybrid binder consisting of 70% alkali activated material and 30% cement applied without NaOH pre-treatment results in a composite with excellent mechanical performances and reduced environmental impacts of 61.5% compared to a pure cement system.

Impact of farmland characteristics on grain costs and benefits in the North China Plain
Wang, Qian ; Qiu, Junjie ; Yu, Jin - \ 2019
Land Use Policy 80 (2019). - ISSN 0264-8377 - p. 142 - 149.
Costs and benefits - Farmland characteristics - Grain production - Multilevel linear model - Plot

Land characteristics in general and socio-economic characteristics in particular are assumed to play important roles in the determination of grain costs and benefits. This study explores the effects of farmland characteristics on grain costs and benefits using a multilevel linear model. The data refer to 1282 grain plots of 566 grain producers in the provinces of Henan, Shandong, and Anhui in the North China Plain. The results show that the coefficients of the variables used to measure plot size and tenure insecurity have different values and signs for households with different grain planted areas. It can be concluded that the effects of plot size and ratio of rented land are closely related to farmers’ total grain planted area, and only farmers with grain areas below 1.33 ha can achieve economies of scale. The effects of tenure insecurity of rented land on grain costs and benefits were negative, but the values became smaller and insignificant when farmers’ total grain area was sufficiently large. Regarding farmland bio-physical characteristics, farmers obtain more profit from plots with water conservancy facilities and have to invest more in poor land, with no output increments.

Water footprint of the energy sector in China's two megalopolises
Liao, Xiawei ; Zhao, Xu ; Jiang, Yu ; Liu, Yu ; Yi, Yujun ; Tillotson, Martin R. - \ 2019
Ecological Modelling 391 (2019). - ISSN 0304-3800 - p. 9 - 15.
Jing-Jin-Ji - Urban - Water footprint - Water-for-energy nexus - Yangtze Delta

Using a consumption-based Multi-Regional Input-Output (MRIO) model, we investigate the distinctive characteristics, self-efficiency or external dependency, of energy demand's water footprint in China's two biggest and fastest developing megalopolises. We find that energy demand water footprint in the Jing-Jin-Ji and the Yangtze Delta amounted to 2.41 and 9.59 billion m³of water withdrawal respectively in 2010, of which 848.06 and 973.91 million m³was consumed. Among all energy products, electricity contributed the largest share to the energy sector's water footprint in both regions. The sectoral distribution of water footprint in the upstream supply chain differed by region. Most significantly, the agricultural sector accounted for more than 30% of water consumption footprint. In addition to water used locally, final energy demands in these two regions induced external water footprint beyond their administrative boundaries. The Jing-Jin-Ji region's energy sector had a smaller water footprint compared to the water-abundant Yangtze Delta region. However, external water footprint occupied a larger proportion in the former. Such divergence can be attributed to the distinctive water endowments and water-using technologies utilized in their respective energy sectors. Bespoke urban governance and policies tailored to local resource and technology portfolios are recommended for different urban agglomeration energy and water flows.

Assessing the influences of ecological restoration on perceptions of cultural ecosystem services by residents of agricultural landscapes of western China
Dou, Yuehan ; Zhen, Lin ; Yu, Xiubo ; Bakker, Martha ; Carsjens, Gerrit Jan ; Xue, Zhichao - \ 2019
Science of the Total Environment 646 (2019). - ISSN 0048-9697 - p. 685 - 695.
Agricultural landscapes - Cultural ecosystem services - Ecological restoration - Household survey - Human perception

Landscape change caused by ecological restoration projects has both positive and negative influences on human livelihoods, yet surprisingly little research on the cultural consequences of ecological restoration in agricultural landscapes has taken place. Cultural consequences can be captured in the ecosystem services framework as cultural ecosystem services (CES). However, assessment and valuation of these services to support decision-making for this essential ecosystem is lacking. To help fill this gap, we assessed the opinions of Chinese rural communities about CES and the changes in their perception under the Grain for Green program (GFG), a nationwide program to relieve the pressure on ecosystems (soil erosion and land degradation) by converting cultivated land or barren land on steep slopes into grassland and forests. We used Guyuan City in China's Ningxia Hui Autonomous Region as a case study, using a workshop to identify the CES provided by the agricultural landscape, followed by semi-structured household interviews to quantify perceptions of these CES. We found that all eight CES types identified by the workshop were perceived by the rural communities. Reforestation changed their perceptions of CES directly due to land cover change and indirectly due to the resulting economic changes and migration of mostly young workers in search of better jobs. Cultivated land was perceived as more important than forest for CES provision. In addition, residential areas were perceived as providing significant CES because of local traditions that produce close and highly social neighborhood bonds in agricultural landscapes.

Hoe haal je medicatie uit water?: Milieutechnologie onderzoekt drie veelbelovende methoden
Langenhoff, Alette ; Lei, Yu - \ 2018
Intercropping potato (Solanum tuberosum L.) with hairy vetch (Vicia villosa) increases water use efficiency in dry conditions
Ren, Jianhong ; Zhang, Lizhen ; Duan, Yu ; Zhang, Jun ; Evers, Jochem B. ; Zhang, Yue ; Su, Zhicheng ; Werf, Wopke van der - \ 2018
Field Crops Research (2018). - ISSN 0378-4290
Biomass - Daily water use - Land equivalent ratio (LER) - Water equivalent ratio (WER) - Water saving

Protection from soil erosion and efficient use of water are vital to sustainable dryland potato production in semi-arid regions. Introducing legumes into semi-arid agricultural systems as intercrops improves soil quality due to biological nitrogen fixation and reduced wind erosion as a result of better soil cover, but the consequences of introducing legumes for the water use efficiency of the crop system are less predictable. Here we carried out field experiments from 2014 to 2017 in Inner Mongolia, China. We compared a rotational intercropping system of potato (Solanum tuberosum L.) and hairy vetch (Vicia villosa) with monocultures of potato and hairy vetch and quantified crop yield, water use efficiency and land productivity. While the relative density (the ratio of plant density in intercrop and the density in sole stand) of both crops in the intercropping was 0.5, the average relative yield of the potato over four years was 0.43, but that of the vetch was 0.87, indicating dominance of the vetch in the intercropping system. Land and water equivalent ratios, defined as the area of land or amount of water that would be needed in single cropping to achieve the same yield as in intercropping, averaged to 1.30 and 1.29 over the years, respectively, indicating high relative land and water productivity of potato/hairy vetch intercropping compared to monocultures. Vetch was a stronger competitor for water than potato with a partial water equivalent ratio of 0.83. We conclude that the potato/vetch intercropping system improves land productivity and system level water use efficiency under the rain-fed semi-arid conditions of the study site. These results are useful to optimize cropping systems for regional sustainability with consideration of both arable crop production (potato) and provision of fodder for animal husbandry (vetch).

Carbon storage potential in degraded forests of Kalimantan, Indonesia
Ferraz, António ; Saatchi, Sassan ; Xu, Liang ; Hagen, Stephen ; Chave, Jerome ; Yu, Yifan ; Meyer, Victoria ; Garcia, Mariano ; Silva, Carlos ; Roswintiart, Orbita ; Samboko, Ari ; Sist, Plinio ; Walker, Sarah ; Pearson, Timothy R.H. ; Wijaya, Arief ; Sullivan, Franklin B. ; Rutishauser, Ervan ; Hoekman, Dirk ; Ganguly, Sangram - \ 2018
Environmental Research Letters 13 (2018)9. - ISSN 1748-9318
aboveground biomass mapping - airborne lidar - carbon - forest degradation - Indonesia - Kalimantan - peat swamp forests

The forests of Kalimantan are under severe pressure from extensive land use activities dominated by logging, palm oil plantations, and peatland fires. To implement the forest moratorium for mitigating greenhouse gas emissions, Indonesia's government requires information on the carbon stored in forests, including intact, degraded, secondary, and peat swamp forests. We developed a hybrid approach of producing a wall-to-wall map of the aboveground biomass (AGB) of intact and degraded forests of Kalimantan at 1 ha grid cells by combining field inventory plots, airborne lidar samples, and satellite radar and optical imagery. More than 110 000 ha of lidar data were acquired to systematically capture variations of forest structure and more than 104 field plots to develop lidar-biomass models. The lidar measurements were converted into biomass using models developed for 66 439 ha of drylands and 44 250 ha of wetland forests. By combining the AGB map with the national land cover map, we found that 22.3 Mha (106 ha) of forest remain on drylands ranging in biomass from 357.2 ±12.3 Mgha-1 in relatively intact forests to 134.2 ±6.1 Mgha-1 in severely degraded forests. The remaining peat swamp forests are heterogeneous in coverage and degradation level, extending over 3.62 Mha and having an average AGB of 211.8 ±12.7 Mgha-1. Emission factors calculated from aboveground biomass only suggest that the carbon storage potential of more than 15 Mha of degraded and secondary dryland forests will be about 1.1 PgC.

Data from: Soil microbes promote complementarity effects among co-existing trees through soil nitrogen partitioning
Luo, Shan ; Schmid, Bernhard ; Deyn, G.B. de; Yu, Shixiao - \ 2018
biodiversity - complementarity - ecosystem functioning - mycorrhizal fungi - nitrogen partitioning - plant-soil interactions - soil microbes
1. Plant resource partitioning is a mechanism promoting species coexistence and ecosystem functioning. Yet, we still have limited understanding of how soil microbes, especially plant symbiotic microbes, influence resource partitioning. We hypothesized that soil borne microbes, in particular mycorrhizal fungi, facilitate differential performance of tree species depending on different nitrogen sources and that this leads to a positive plant diversity–community productivity relationship. 2. We conducted two complementing glasshouse experiments. In a “monoculture experiment”, we supplied nitrogen as ammonium, nitrate or glycine and tested the growth response of three tree species associated with different root symbionts: one associated with ectomycorrhizal fungi, one associated with arbuscular mycorrhizal fungi and the third associated with both arbuscular mycorrhizal fungi and N-fixing bacteria. In an “intermixed experiment”, we grew the tree species at three richness levels (one, two or three species) in soil supplied with a mix of the three nitrogen forms or no added nitrogen, and with or without soil microbes. 3. The monoculture experiment showed that in the presence of soil microbes, the ectomycorrhizal plant species grew best when supplied with glycine and the two arbuscular mycorrhizal plant species grew best with either nitrate or ammonium addition. When the different forms of nitrogen were mixed in the intermixed experiment, plant mixtures produced more biomass than plant monocultures in the presence of soil microbes, with positive complementarity effects indicating microbe-mediated plant resource partitioning. 4. Our results suggest that co-existing tree species can partition soil nitrogen when grown with their particular mycorrhizal symbionts or other soil microbes, resulting in positive biodiversity effects in complex resource environments.
Fatty acid biomarkers of dairy fat consumption and incidence of type 2 diabetes : A pooled analysis of prospective cohort studies
Imamura, Fumiaki ; Fretts, Amanda ; Marklund, Matti ; Ardisson Korat, Andres V. ; Yang, Wei Sin ; Lankinen, Maria ; Qureshi, Waqas ; Helmer, Catherine ; Chen, Tzu An ; Wong, Kerry ; Bassett, Julie K. ; Murphy, Rachel ; Tintle, Nathan ; Yu, Chaoyu Ian ; Brouwer, Ingeborg A. ; Chien, Kuo Liong ; Frazier-Wood, Alexis C. ; Gobbo, Liana C. Del; Djoussé, Luc ; Geleijnse, Johanna M. ; Giles, Graham G. ; Goede, Janette de; Gudnason, Vilmundur ; Harris, William S. ; Hodge, Allison ; Hu, Frank ; Koulman, Albert ; Laakso, Markku ; Lind, Lars ; Lin, Hung Ju ; McKnight, Barbara ; Rajaobelina, Kalina ; Risérus, Ulf ; Robinson, Jennifer G. ; Samieri, Cécilia ; Siscovick, David S. ; Soedamah-Muthu, Sabita S. ; Sotoodehnia, Nona ; Sun, Qi ; Tsai, Michael Y. ; Uusitupa, Matti ; Wagenknecht, Lynne E. ; Wareham, Nick J. ; Wu, Jason Hy ; Micha, Renata ; Forouhi, Nita G. ; Lemaitre, Rozenn N. ; Mozaffarian, Dariush - \ 2018
PLOS Medicine 15 (2018)10. - ISSN 1549-1676

BACKGROUND: We aimed to investigate prospective associations of circulating or adipose tissue odd-chain fatty acids 15:0 and 17:0 and trans-palmitoleic acid, t16:1n-7, as potential biomarkers of dairy fat intake, with incident type 2 diabetes (T2D).

METHODS AND FINDINGS: Sixteen prospective cohorts from 12 countries (7 from the United States, 7 from Europe, 1 from Australia, 1 from Taiwan) performed new harmonised individual-level analysis for the prospective associations according to a standardised plan. In total, 63,682 participants with a broad range of baseline ages and BMIs and 15,180 incident cases of T2D over the average of 9 years of follow-up were evaluated. Study-specific results were pooled using inverse-variance-weighted meta-analysis. Prespecified interactions by age, sex, BMI, and race/ethnicity were explored in each cohort and were meta-analysed. Potential heterogeneity by cohort-specific characteristics (regions, lipid compartments used for fatty acid assays) was assessed with metaregression. After adjustment for potential confounders, including measures of adiposity (BMI, waist circumference) and lipogenesis (levels of palmitate, triglycerides), higher levels of 15:0, 17:0, and t16:1n-7 were associated with lower incidence of T2D. In the most adjusted model, the hazard ratio (95% CI) for incident T2D per cohort-specific 10th to 90th percentile range of 15:0 was 0.80 (0.73-0.87); of 17:0, 0.65 (0.59-0.72); of t16:1n7, 0.82 (0.70-0.96); and of their sum, 0.71 (0.63-0.79). In exploratory analyses, similar associations for 15:0, 17:0, and the sum of all three fatty acids were present in both genders but stronger in women than in men (pinteraction < 0.001). Whereas studying associations with biomarkers has several advantages, as limitations, the biomarkers do not distinguish between different food sources of dairy fat (e.g., cheese, yogurt, milk), and residual confounding by unmeasured or imprecisely measured confounders may exist.

CONCLUSIONS: In a large meta-analysis that pooled the findings from 16 prospective cohort studies, higher levels of 15:0, 17:0, and t16:1n-7 were associated with a lower risk of T2D.

Denitrification-potential evaluation and nitrate-removal-pathway analysis of aerobic denitrifier strain Marinobacter hydrocarbonoclasticus RAD-2
Kong, Dedong ; Li, Wenbing ; Deng, Yale ; Ruan, Yunjie ; Chen, Guangsuo ; Yu, Jianhai ; Lin, Fucheng - \ 2018
Water 10 (2018)10. - ISSN 2073-4441
Aerobic denitrification - Denitrifying gene expression - Marinobacter hydrocarbonoclasticus RAD-2 - Nitrogen removal - Wastewater treatment

An aerobic denitrifier was isolated from a long-term poly (3-hydroxybutyrate-co-3- hydroxyvalerate) PHBV-supported denitrification reactor that operated under alternate aerobic/anoxic conditions. The strain was identified as Marinobacter hydrocarbonoclasticus RAD-2 based on 16S rRNA-sequence phylogenetic analysis. Morphology was observed by scanning electron microscopy (SEM), and phylogenetic characteristics were analyzed with the API 20NE test. Strain RAD-2 showed efficient aerobic denitrification ability when using NO3 - -N or NO2 --N as its only nitrogen source, while heterotrophic nitrification was not detected. The average NO3 --N and NO2 --N removal rates were 6.47 mg/(L·h)and 6.32 mg/(L·h), respectively. Single-factor experiments indicated that a 5:10 C/N ratio, 25-40 °C temperature, and 100-150 rpm rotation speed were the optimal conditions for aerobic denitrification. Furthermore, the denitrifying gene napA had the highest expression on a transcriptional level, followed by the denitrifying genes nirS and nosZ. The norB gene was found to have significantly low expression during the experiment. Overall, great aerobic denitrification ability makes the RAD-2 strain a potential alternative in enhancing nitrate management for marine recirculating aquaculture system (RAS) practices.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa
Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
The red bayberry genome and genetic basis of sex determination
Jia, Hui Min ; Jia, Hui Juan ; Cai, Qing Le ; Wang, Yan ; Zhao, Hai Bo ; Yang, Wei Fei ; Wang, Guo Yun ; Li, Ying Hui ; Zhan, Dong Liang ; Shen, Yu Tong ; Niu, Qing Feng ; Chang, Le ; Qiu, Jie ; Zhao, Lan ; Xie, Han Bing ; Fu, Wan Yi ; Jin, Jing ; Li, Xiong Wei ; Jiao, Yun ; Zhou, Chao Chao ; Tu, Ting ; Chai, Chun Yan ; Gao, Jin Long ; Fan, Long Jiang ; Weg, Eric van de; Wang, Jun Yi ; Gao, Zhong Shan - \ 2018
Plant Biotechnology Journal (2018). - ISSN 1467-7644
genome - Morella rubra - sex-determining region - sex-linked marker

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding
Eeuwijk, Fred A. van; Bustos-Korts, Daniela ; Millet, Emilie J. ; Boer, Martin P. ; Kruijer, Willem ; Thompson, Addie ; Malosetti, Marcos ; Iwata, Hiroyoshi ; Quiroz, Roberto ; Kuppe, Christian ; Muller, Onno ; Blazakis, Konstantinos N. ; Yu, Kang ; Tardieu, Francois ; Chapman, Scott C. - \ 2018
Plant Science (2018). - ISSN 0168-9452
Crop growth model - Genomic prediction - Genotype-by-environment-interaction - Genotype-to-phenotype model - Mixed model - Multi-environment model - Multi-trait model - Phenotyping - Phenotyping platform - Physiology - Plant breeding - Prediction - Reaction norm - Response surface - Statistical genetics

New types of phenotyping tools generate large amounts of data on many aspects of plant physiology and morphology with high spatial and temporal resolution. These new phenotyping data are potentially useful to improve understanding and prediction of complex traits, like yield, that are characterized by strong environmental context dependencies, i.e., genotype by environment interactions. For an evaluation of the utility of new phenotyping information, we will look at how this information can be incorporated in different classes of genotype-to-phenotype (G2P) models. G2P models predict phenotypic traits as functions of genotypic and environmental inputs. In the last decade, access to high-density single nucleotide polymorphism markers (SNPs) and sequence information has boosted the development of a class of G2P models called genomic prediction models that predict phenotypes from genome wide marker profiles. The challenge now is to build G2P models that incorporate simultaneously extensive genomic information alongside with new phenotypic information. Beyond the modification of existing G2P models, new G2P paradigms are required. We present candidate G2P models for the integration of genomic and new phenotyping information and illustrate their use in examples. Special attention will be given to the modelling of genotype by environment interactions. The G2P models provide a framework for model based phenotyping and the evaluation of the utility of phenotyping information in the context of breeding programs.

Symposium review: Uncertainties in enteric methane inventories, measurement techniques, and prediction models
Hristov, A.N. ; Kebreab, Ermias ; Niu, Mutian ; Oh, J. ; Bannink, A. ; Bayat, Ali R. ; Boland, Tommy ; Brito, A.F. ; Casper, D.P. ; Crompton, Les A. ; Dijkstra, J. ; Eugène, Maguy A. ; Garnsworthy, Phil C. ; Haque, N. ; Hellwing, Anne L.F. ; Huhtanen, Pekka ; Kreuzer, Michael ; Lund, Peter ; Madsen, Jørgen ; Martin, C. ; Moate, P.J. ; Muetzel, Stefan ; Muñoz, Camila ; Peiren, Nico ; Powell, J.M. ; Reynolds, Chris ; Schwarm, Angela ; Shingfield, Kevin J. ; Storlien, Tonje M. ; Weisbjerg, Martin Riis ; Yáñez-Ruiz, D.R. ; Yu, Z. - \ 2018
Journal of Dairy Science 101 (2018)7. - ISSN 0022-0302 - p. 6655 - 6674.
Ruminant production systems are important contributors to anthropogenic methane (CH4) emissions, but there are large uncertainties in national and global livestock CH4 inventories. Sources of uncertainty in enteric CH4 emissions include animal inventories, feed dry matter intake (DMI), ingredient and chemical composition of the diets, and CH4 emission factors. There is also significant uncertainty associated with enteric CH4 measurements. The most widely used techniques are respiration chambers, the sulfur hexafluoride (SF6) tracer technique, and the automated head-chamber system (GreenFeed; C-Lock Inc., Rapid City, SD). All 3 methods have been successfully used in a large number of experiments with dairy or beef cattle in various environmental conditions, although studies that compare techniques have reported inconsistent results. Although different types of models have been developed to predict enteric CH4 emissions, relatively simple empirical (statistical) models have been commonly used for inventory purposes because of their broad applicability and ease of use compared with more detailed empirical and process-based mechanistic models. However, extant empirical models used to predict enteric CH4 emissions suffer from narrow spatial focus, limited observations, and limitations of the statistical technique used. Therefore, prediction models must be developed from robust data sets that can only be generated through collaboration of scientists across the world. To achieve high prediction accuracy, these data sets should encompass a wide range of diets and production systems within regions and globally. Overall, enteric CH4 prediction models are based on various animal or feed characteristic inputs but are dominated by DMI in one form or another. As a result, accurate prediction of DMI is essential for accurate prediction of livestock CH4 emissions. Analysis of a large data set of individual dairy cattle data showed that simplified enteric CH4 prediction models based on DMI alone or DMI and limited feed- or animal-related inputs can predict average CH4 emission with a similar accuracy to more complex empirical models. These simplified models can be reliably used for emission inventory purposes.
The burden of cardiovascular diseases among us states, 1990-2016
Roth, Gregory A. ; Johnson, Catherine O. ; Abate, Kalkidan Hassen ; Abd-Allah, Foad ; Ahmed, Muktar ; Alam, Khurshid ; Alam, Tahiya ; Alvis-Guzman, Nelson ; Ansari, Hossein ; Ärnlöv, Johan ; Atey, Tesfay Mehari ; Awasthi, Ashish ; Awoke, Tadesse ; Barac, Aleksandra ; Bärnighausen, Till ; Bedi, Neeraj ; Bennett, Derrick ; Bensenor, Isabela ; Biadgilign, Sibhatu ; Castañeda-Orjuela, Carlos ; Catalá-López, Ferrán ; Davletov, Kairat ; Dharmaratne, Samath ; Ding, Eric L. ; Dubey, Manisha ; Faraon, Emerito Jose Aquino ; Farid, Talha ; Farvid, Maryam S. ; Feigin, Valery ; Fernandes, João ; Frostad, Joseph ; Gebru, Alemseged ; Geleijnse, Johanna M. ; Gona, Philimon Nyakauru ; Griswold, Max ; Hailu, Gessessew Bugssa ; Hankey, Graeme J. ; Hassen, Hamid Yimam ; Havmoeller, Rasmus ; Hay, Simon ; Heckbert, Susan R. ; Irvine, Caleb Mackay Salpeter ; James, Spencer Lewis ; Jara, Dube ; Kasaeian, Amir ; Khan, Abdur Rahman ; Khera, Sahil ; Khoja, Abdullah T. ; Khubchandani, Jagdish ; Kim, Daniel ; Kolte, Dhaval ; Lal, Dharmesh ; Larsson, Anders ; Linn, Shai ; Lotufo, Paulo A. ; Razek, Hassan Magdy Abd El; Mazidi, Mohsen ; Meier, Toni ; Mendoza, Walter ; Mensah, George A. ; Meretoja, Atte ; Mezgebe, Haftay Berhane ; Mirrakhimov, Erkin ; Mohammed, Shafiu ; Moran, Andrew Edward ; Nguyen, Grant ; Nguyen, Minh ; Ong, Kanyin Liane ; Owolabi, Mayowa ; Pletcher, Martin ; Pourmalek, Farshad ; Purcell, Caroline A. ; Qorbani, Mostafa ; Rahman, Mahfuzar ; Rai, Rajesh Kumar ; Ram, Usha ; Reitsma, Marissa Bettay ; Renzaho, Andre M.N. ; Rios-Blancas, Maria Jesus ; Safiri, Saeid ; Salomon, Joshua A. ; Sartorius, Benn ; Sepanlou, Sadaf Ghajarieh ; Shaikh, Masood Ali ; Silva, Diego ; Stranges, Saverio ; Tabarés-Seisdedos, Rafael ; Atnafu, Niguse Tadele ; Thakur, J.S. ; Topor-Madry, Roman ; Truelsen, Thomas ; Tuzcu, E.M. ; Tyrovolas, Stefanos ; Ukwaja, Kingsley Nnanna ; Vasankari, Tommi ; Vlassov, Vasiliy ; Vollset, Stein Emil ; Wakayo, Tolassa ; Weintraub, Robert ; Wolfe, Charles ; Workicho, Abdulhalik ; Xu, Gelin ; Yadgir, Simon ; Yano, Yuichiro ; Yip, Paul ; Yonemoto, Naohiro ; Younis, Mustafa ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Zipkin, Ben ; Afshin, Ashkan ; Gakidou, Emmanuela ; Lim, Stephen S. ; Mokdad, Ali H. ; Naghavi, Mohsen ; Vos, Theo ; Murray, Christopher J.L. - \ 2018
JAMA Cardiology 3 (2018)5. - ISSN 2380-6583 - p. 375 - 389.
Importance: Cardiovascular disease (CVD) is the leading cause of death in the United States, but regional variation within the United States is large. Comparable and consistent state-level measures of total CVD burden and risk factors have not been produced previously. Objective: To quantify and describe levels and trends of lost health due to CVD within the United States from 1990 to 2016 as well as risk factors driving these changes. Design, setting, and participants: Using the Global Burden of Disease methodology, cardiovascular disease mortality, nonfatal health outcomes, and associated risk factors were analyzed by age group, sex, and year from 1990 to 2016 for all residents in the United States using standardized approaches for data processing and statistical modeling. Burden of disease was estimated for 10 groupings of CVD, and comparative risk analysis was performed. Data were analyzed from August 2016 to July 2017. Exposures: Residing in the United States. Main outcomes ans measures: Cardiovascular disease disability-Adjusted life-years (DALYs). Results: Between 1990 and 2016, age-standardized CVD DALYs for all states decreased. Several states had large rises in their relative rank ordering for total CVD DALYs among states, including Arkansas, Oklahoma, Alabama, Kentucky, Missouri, Indiana, Kansas, Alaska, and Iowa. The rate of decline varied widely across states, and CVD burden increased for a small number of states in the most recent years. Cardiovascular disease DALYs remained twice as large among men compared with women. Ischemic heart disease was the leading cause of CVD DALYs in all states, but the second most common varied by state. Trends were driven by 12 groups of risk factors, with the largest attributable CVD burden due to dietary risk exposures followed by high systolic blood pressure, high body mass index, high total cholesterol level, high fasting plasma glucose level, tobacco smoking, and low levels of physical activity. Increases in risk-deleted CVD DALY rates between 2006 and 2016 in 16 states suggest additional unmeasured risks beyond these traditional factors. Conclusions and relevance: Large disparities in total burden of CVD persist between US states despite marked improvements in CVD burden. Differences in CVD burden are largely attributable to modifiable risk exposures.
The importance of surface reflectance anisotropy for cloud and NO2 retrievals from GOME-2 and OMI
Lorente, Alba ; Boersma, K.F. ; Stammes, Piet ; Tilstra, L.G. ; Richter, Andreas ; Yu, Huan ; Kharbouche, Said ; Muller, Jan Peter - \ 2018
Atmospheric Measurement Techniques 11 (2018)7. - ISSN 1867-1381 - p. 4509 - 4529.

The angular distribution of the light reflected by the Earth's surface influences top-of-atmosphere (TOA) reflectance values. This surface reflectance anisotropy has implications for UV/Vis satellite retrievals of albedo, clouds, and trace gases such as nitrogen dioxide (NO2). These retrievals routinely assume the surface to reflect light isotropically. Here we show that cloud fractions retrieved from GOME-2A and OMI with the FRESCO and OMCLDO2 algorithms have an east-west bias of 10% to 50 %, which are highest over vegetation and forested areas, and that this bias originates from the assumption of isotropic surface reflection. To interpret the across-track bias with the DAK radiative transfer model, we implement the bidirectional reflectance distribution function (BRDF) from the Ross-Li semi-empirical model. Testing our implementation against state-of-the-art RTMs LIDORT and SCIATRAN, we find that simulated TOA reflectance generally agrees to within 1 %. We replace the assumption of isotropic surface reflection in the equations used to retrieve cloud fractions over forested scenes with scattering kernels and corresponding BRDF parameters from a daily high-resolution database derived from 16 years' worth of MODIS measurements. By doing this, the east-west bias in the simulated cloud fractions largely vanishes. We conclude that across-track biases in cloud fractions can be explained by cloud algorithms that do not adequately account for the effects of surface reflectance anisotropy. The implications for NO2 air mass factor (AMF) calculations are substantial. Under moderately polluted NO2 and backwardscattering conditions, clear-sky AMFs are up to 20% higher and cloud radiance fractions up to 40% lower if surface anisotropic reflection is accounted for. The combined effect of these changes is that NO2 total AMFs increase by up to 30% for backward-scattering geometries (and decrease by up to 35% for forward-scattering geometries), which is stronger than the effect of either contribution alone. In an unpolluted troposphere, surface BRDF effects on cloud fraction counteract (and largely cancel) the effect on the clearsky AMF. Our results emphasise that surface reflectance anisotropy needs to be taken into account in a coherent manner for more realistic and accurate retrievals of clouds and NO2 from UV/Vis satellite sensors. These improvements will be beneficial for current sensors, in particular for the recently launched TROPOMI instrument with a high spatial resolution.

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