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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Propagating annotations of molecular networks using in silico fragmentation
Silva, Ricardo R. da; Wang, Mingxun ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Fox, Evan ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Lopes, Norberto Peporine ; Dorrestein, Pieter C. - \ 2018
PLoS Computational Biology 14 (2018)4. - ISSN 1553-734X

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Hotspots for Nitrogen and Phosphorus Losses from Food Production in China : A County-Scale Analysis
Wang, M. ; Ma, L. ; Strokal, M. ; Ma, Wenqi ; Liu, Xuejun ; Kroeze, C. - \ 2018
Environmental Science and Technology (2018). - ISSN 0013-936X
Food production in China results in large losses of nitrogen (N) and phosphorus (P) to the environment. Our objective is to identify hotspots for N and P losses to the environment from food production in China at the county scale. To do this, we used the NUFER (Nutrient flows in Food chains, Environment and Resources use) model. Between 1990 and 2012, the hotspot area expanded by a factor of 3 for N, and 24 for P. In 2012 most hotspots were found in the North China Plain. Hotspots covered less than 10% of the Chinese land area, but contributed by more than half to N and P losses to the environment. Direct discharge of animal manure to rivers was an important cause of N and P losses. Food production was found to be more intensive in hotspots than in other counties. Synthetic fertilizer use and animal numbers in hotspots were a factor of 4–5 higher than in other counties in 2012. Also the number of people working in food production and the incomes of farmers are higher in hotspots than in other counties. This study concludes with suggestions for region-specific pollution control technologies for food production in China.
The Ozone Monitoring Instrument : Overview of 14 years in space
Levelt, Pieternel F. ; Joiner, Joanna ; Tamminen, Johanna ; Veefkind, J.P. ; Bhartia, Pawan K. ; Zweers, Deborah C.S. ; Duncan, Bryan N. ; Streets, David G. ; Eskes, Henk ; Der, Ronald A. Van; McLinden, Chris ; Fioletov, Vitali ; Carn, Simon ; Laat, Jos De; Deland, Matthew ; Marchenko, Sergey ; McPeters, Richard ; Ziemke, Jerald ; Fu, Dejian ; Liu, Xiong ; Pickering, Kenneth ; Apituley, Arnoud ; Abad, Gonzalo González ; Arola, Antti ; Boersma, Folkert ; Miller, Christopher Chan ; Chance, Kelly ; Graaf, Martin De; Hakkarainen, Janne ; Hassinen, Seppo ; Ialongo, Iolanda ; Kleipool, Quintus ; Krotkov, Nickolay ; Li, Can ; Lamsal, Lok ; Newman, Paul ; Nowlan, Caroline ; Suleiman, Raid ; Tilstra, Lieuwe Gijsbert ; Torres, Omar ; Wang, Huiqun ; Wargan, Krzysztof - \ 2018
Atmospheric Chemistry and Physics 18 (2018)8. - ISSN 1680-7316 - p. 5699 - 5745.
This overview paper highlights the successes of the Ozone Monitoring Instrument (OMI) on board the Aura satellite spanning a period of nearly 14 years. Data from OMI has been used in a wide range of applications and research resulting in many new findings. Due to its unprecedented spatial resolution, in combination with daily global coverage, OMI plays a unique role in measuring trace gases important for the ozone layer, air quality, and climate change. With the operational very fast delivery (VFD; direct readout) and near real-time (NRT) availability of the data, OMI also plays an important role in the development of operational services in the atmospheric chemistry domain.
The preferential retention of VIZn over IVZn on birnessite during dissolution/desorption
Qin, Zhangjie ; Yin, Hui ; Wang, Xiaoming ; Zhang, Qin ; Lan, Shuai ; Koopal, Luuk K. ; Zheng, Lirong ; Feng, Xionghan ; Liu, Fan - \ 2018
Applied Clay Science 161 (2018). - ISSN 0169-1317 - p. 169 - 175.
Birnessite - Desorption - Dissolution - Extended X-ray absorption fine structure spectroscopy - Zinc coordination
Zn is a common heavy metal in soils and sediments. In this study, the release behaviors of octahedral (VIZn) and tetrahedral (IVZn) Zn complexes on synthesized hexagonal birnessite were explored by solution chemistry method in combination with spectroscopic analysis. In acidic dissolution processes, the release of adsorbed Zn2+ from birnessite occurred into two stages: in the first stage, ~60% of Zn2+ was desorbed rapidly, with only 8% of Mn being released, and the ratio of VIZn/IVZn increased with time; in the second stage, the residual Zn2+ was mostly VIZn and released slowly at a nearly constant rate until complete dissolution of the matrix mineral was observed. During desorption of Zn2+ by Pb2+, the ratio of VIZn/IVZn on birnessite also increased, while the residual percentage of VIZn remained nearly constant. However, it is known that IVZn-triple corner-sharing (TCS) is more stable than VIZn-TCS, suggesting that part of the remaining IVZn-TCS on birnessite might transform to VIZn-TCS immediately when VIZn-TCS is replaced by H+ or Pb2+. Additionally, the possible distribution of Mn3+ and IVZn or the partial charge compensation by protons can lead to the preferential retention of VIZn on birnessite or the preferential re-adsorption of VIZn at the new edge sites. These results can provide new insights into the geochemical behavior of Zn2+ contaminant in soil and aquatic environments.
Geographically weighted area-to-point regression kriging for spatial downscaling in remote sensing
Jin, Yan ; Ge, Yong ; Wang, Jianghao ; Heuvelink, Gerard B.M. ; Wang, Le - \ 2018
Remote Sensing 10 (2018)4. - ISSN 2072-4292
High-resolution imaging - Soil moisture - Spatial downscaling
Spatial downscaling of remotely sensed products is one of the main ways to obtain earth observations at fine resolution. Area-to-point (ATP) geostatistical techniques, in which regular fine grids of remote sensing products are regarded as points, have been applied widely for spatial downscaling. In spatial downscaling, it is common to use auxiliary information to explain some of the unknown spatial variation of the target geographic variable. Because of the ubiquitously spatial heterogeneities, the observed variables always exhibit uncontrolled variance. To overcome problems caused by local heterogeneity that cannot meet the stationarity requirement in ATP regression kriging, this paper proposes a hybrid spatial statistical method which incorporates geographically weighted regression and ATP kriging for spatial downscaling. The proposed geographically weighted ATP regression kriging (GWATPRK) combines fine spatial resolution auxiliary information and allows for non-stationarity in a downscaling model. The approach was verified using eight groups of four different 25 km-resolution surface soil moisture (SSM) remote sensing products to obtain 1 km SSM predictions in two experimental regions, in conjunction with the implementation of three benchmark methods. Analyses and comparisons of the different downscaled results showed GWATPRK obtained downscaled fine spatial resolution images with greater quality and an average loss with a root mean square error value of 17.5%. The analysis indicated the proposed method has high potential for spatial downscaling in remote sensing applications.
Major threats of pollution and climate change to global coastal ecosystems and enhanced management for sustainability
Lu, Y. ; Yuan, J. ; Lu, X. ; Su, Chao ; Zhang, Y. ; Wang, C. ; Cao, X. ; Li, Q. ; Su, Jilan ; Ittekkot, Venugopalan ; Garbutt, Richard Angus ; Bush, S.R. ; Fletcher, Stephen ; Wagey, Tonny ; Kachur, Anatolii ; Sweijd, Neville - \ 2018
Environmental Pollution 239 (2018). - ISSN 0269-7491 - p. 670 - 680.
coastal ecosystem - marine pollution - climate change - ecological impacts - coastal sustainability
Coastal zone is of great importance in the provision of various valuable ecosystem services. However, it is also sensitive and vulnerable to environmental changes due to high human populations and interactions between the land and ocean. Major threats of pollution from over enrichment of nutrients, increasing metals and persistent organic pollutants (POPs), and climate change have led to severe ecological degradation in the coastal zone, while few studies have focused on the combined impacts of pollution and climate change on the coastal ecosystems at the global level. A global overview of nutrients, metals, POPs, and major environmental changes due to climate change and their impacts on coastal ecosystems was carried out in this study. Coasts of the Eastern Atlantic and Western Pacific were hotspots of concentrations of several pollutants, and mostly affected by warming climate. These hotspots shared the same features of large populations, heavy industry and (semi-) closed sea. Estimation of coastal ocean capital, integrated management of land-ocean interaction in the coastal zone, enhancement of integrated global observation system, and coastal ecosystem-based management can play effective roles in promoting sustainable management of coastal marine ecosystems. Enhanced management from the perspective of mitigating pollution and climate change was proposed.
The Hot Serial Cereal Experiment for modeling wheat response to temperature: field experiments and AgMIP-Wheat multi-model simulations
Martre, Pierre ; Kimball, Bruce A. ; Ottman, Michael J. ; Wall, Gerard W. ; White, Jeffrey W. ; Asseng, Senthold ; Ewert, Frank ; Cammarano, Davide ; Maiorano, Andrea ; Aggarwal, Pramod K. ; Anothai, Jakarat ; Basso, Bruno ; Biernath, Christian ; Challinor, Andrew J. ; Sanctis, Giacomo De; Doltra, Jordi ; Dumont, Benjamin ; Fereres, Elias ; Garcia-Vila, Margarita ; Gayler, Sebastian ; Hoogenboom, Gerrit ; Hunt, Leslie A. ; Izaurralde, Roberto C. ; Jabloun, Mohamed ; Jones, Curtis D. ; Kassie, Belay T. ; Kersebaum, Kurt C. ; Koehler, Ann-Kristin ; Müller, Christoph ; Kumar, Soora Naresh ; Liu, Bing ; Lobell, David B. ; Nendel, Claas ; O'Leary, Garry ; Olesen, Jørgen E. ; Palosuo, Taru ; Priesack, Eckart ; Rezaei, Ehsan Eyshi ; Ripoche, Dominique ; Rötter, Reimund P. ; Semenov, Mikhail A. ; Stöckle, Claudio ; Stratonovitch, Pierre ; Streck, Thilo ; Supit, Iwan ; Tao, Fulu ; Thorburn, Peter ; Waha, Katharina ; Wang, Enli ; Wolf, Joost ; Zhao, Zhigan ; Zhu, Yan - \ 2018
ODjAR : open data journal for agricultural research 4 (2018). - ISSN 2352-6378 - p. 28 - 34.
The data set reported here includes the part of a Hot Serial Cereal Experiment (HSC) experiment recently used in the AgMIP-Wheat project to analyze the uncertainty of 30 wheat models and quantify their response to temperature. The HSC experiment was conducted in an open-field in a semiarid environment in the southwest USA. The data reported herewith include one hard red spring wheat cultivar (Yecora Rojo) sown approximately every six weeks from December to August for a two-year period for a total of 11 planting dates out of the 15 of the entire HSC experiment. The treatments were chosen to avoid any effect of frost on grain yields. On late fall, winter and early spring plantings temperature free-air controlled enhancement (T-FACE) apparatus utilizing infrared heaters with supplemental irrigation were used to increase air temperature by 1.3°C/2.7°C (day/night) with conditions equivalent to raising air temperature at constant relative humidity (i.e. as expected with global warming) during the whole crop growth cycle. Experimental data include local daily weather data, soil characteristics and initial conditions, detailed crop measurements taken at three growth stages during the growth cycle, and cultivar information. Simulations include both daily in-season and end-of-season results from 30 wheat models.
Taxonomy of the family Arenaviridae and the order Bunyavirales : update 2018
Maes, Piet ; Alkhovsky, Sergey V. ; Bào, Yīmíng ; Beer, Martin ; Birkhead, Monica ; Briese, Thomas ; Buchmeier, Michael J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, Christopher S. ; Torre, Juan Carlos de la; Delwart, Eric ; DeRisi, Joseph L. ; Bello, Patrick L. Di; Serio, Francesco Di; Digiaro, Michele ; Dolja, Valerian V. ; Drosten, Christian ; Druciarek, Tobiasz Z. ; Du, Jiang ; Ebihara, Hideki ; Elbeaino, Toufic ; Gergerich, Rose C. ; Gillis, Amethyst N. ; Gonzalez, Jean Paul J. ; Haenni, Anne Lise ; Hepojoki, Jussi ; Hetzel, Udo ; Hồ, Thiện ; Hóng, Ní ; Jain, Rakesh K. ; Jansen van Vuren, Petrus ; Jin, Qi ; Jonson, Miranda Gilda ; Junglen, Sandra ; Keller, Karen E. ; Kemp, Alan ; Kipar, Anja ; Kondov, Nikola O. ; Koonin, Eugene V. ; Kormelink, Richard ; Korzyukov, Yegor ; Krupovic, Mart ; Lambert, Amy J. ; Laney, Alma G. ; LeBreton, Matthew ; Lukashevich, Igor S. ; Marklewitz, Marco ; Markotter, Wanda ; Martelli, Giovanni P. ; Martin, Robert R. ; Mielke-Ehret, Nicole ; Mühlbach, Hans Peter ; Navarro, Beatriz ; Ng, Terry Fei Fan ; Nunes, Márcio Roberto Teixeira ; Palacios, Gustavo ; Pawęska, Janusz T. ; Peters, Clarence J. ; Plyusnin, Alexander ; Radoshitzky, Sheli R. ; Romanowski, Víctor ; Salmenperä, Pertteli ; Salvato, Maria S. ; Sanfaçon, Hélène ; Sasaya, Takahide ; Schmaljohn, Connie ; Schneider, Bradley S. ; Shirako, Yukio ; Siddell, Stuart ; Sironen, Tarja A. ; Stenglein, Mark D. ; Storm, Nadia ; Sudini, Harikishan ; Tesh, Robert B. ; Tzanetakis, Ioannis E. ; Uppala, Mangala ; Vapalahti, Olli ; Vasilakis, Nikos ; Walker, Peter J. ; Wáng, Guópíng ; Wáng, Lìpíng ; Wáng, Yànxiăng ; Wèi, Tàiyún ; Wiley, Michael R. ; Wolf, Yuri I. ; Wolfe, Nathan D. ; Wú, Zhìqiáng ; Xú, Wénxìng ; Yang, Li ; Yāng, Zuòkūn ; Yeh, Shyi Dong ; Zhāng, Yǒng Zhèn ; Zhèng, Yàzhōu ; Zhou, Xueping ; Zhū, Chénxī ; Zirkel, Florian ; Kuhn, Jens H. - \ 2018
Archives of Virology (2018). - ISSN 0304-8608 - p. 1 - 16.
In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
The group I alphabaculovirus-specific protein, AC5, is a novel component of the occlusion body but is not associated with ODVS or the PIF complex
Wang, Xi ; Chen, Cheng ; Zhang, Nan ; Li, Jiang ; Deng, Fei ; Wang, Hualin ; Vlak, Just M. ; Hu, Zhihong ; Wang, Manli - \ 2018
Journal of General Virology 99 (2018)4. - ISSN 0022-1317 - p. 585 - 595.
Ac5 - Baculovirus - Function - Group I alphabaculovirus - Occlusion body - PIF complex
Autographa californica nucleopolyhedrovirus (AcMNPV) orf5 (ac5) is a group I alphabaculovirus-specific gene of unknown function, although the protein (AC5) was previously reported to be associated with the per os infectivity factor (PIF) complex. The purpose of this study was to study the dynamics of AC5 during AcMNPV infection and to verify whether it is indeed a component of the PIF complex. Transcription and expression analyses suggested that ac5 is a late viral gene. An ac5-deleted recombinant AcMNPV was generated by homologous recombination. A one-step growth curve assay indicated that ac5 was not required for budded virus (BV) production in Sf9 cells. Scanning electron microscopy and transmission electron microscopy demonstrated that the deletion of ac5 did not affect occlusion body (OB) morphology, and nor did it affect the insertion of occlusion-derived virus (ODV) into OBs. Partially denaturing SDS-PAGE and a co-immunoprecipitation assay clearly showed that AC5 was not a component of the PIF complex, while the deletion of ac5 did not affect the formation and presence of the PIF complex. Further analyses showed, however, that AC5 was an OB-specific protein, but it was not detected as a component of BVs or ODVs. Bioassay experiments showed that the oral infectivity of ac5-deleted AcMNPV to third instar Spodoptera exigua larvae was not significantly different from that of the ac5-repaired virus. In conclusion, AC5 is an intrinsic protein of OBs, instead of being a component of the PIF complex, and is not essential for either BV or ODV infection. AC5 is awaiting the assignment of another hitherto unknown function.
Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens
Jia, Junjing ; Ahmed, Irfan ; Liu, Lixian ; Liu, Yong ; Xu, Zhiqiang ; Duan, Xiaohua ; Li, Qihua ; Dou, Tengfei ; Gu, Dahai ; Rong, Hua ; Wang, Kun ; Li, Zhengtian ; Talpur, Mir Zulqarnain ; Huang, Ying ; Wang, Shanrong ; Yan, Shixiong ; Tong, Huiquan ; Zhao, Sumei ; Zhao, Guiping ; Pas, Marinus F.W. te; Su, Zhengchang ; Ge, Changrong - \ 2018
PLoS One 13 (2018)4. - ISSN 1932-6203
The growth hormone / insulin-like growth factor-1 (GH/IGF-1) pathway of the somatotropic axis is the major controller for growth rate and body size in vertebrates, but the effect of selection on the expression of GH/IGF-1 somatotropic axis genes and their association with body size and growth performance in farm animals is not fully understood. We analyzed a time series of expression profiles of GH/IGF-1 somatotropic axis genes in two chicken breeds, the Daweishan mini chickens and Wuding chickens, and the commercial Avian broilers hybrid exhibiting markedly different body sizes and growth rates. We found that growth rate and feed conversion efficiency in Daweishan mini chickens were significantly lower than those in Wuding chickens and Avian broilers. The Wuding and Daweishan mini chickens showed higher levels of plasma GH, pituitary GH mRNA but lower levels of hepatic growth hormone receptor (GHR) mRNA than in Avian broilers. Daweishan mini chickens showed significantly lower levels of plasma IGF-1, thigh muscle and hepatic IGF-1 mRNA than did Avian broilers and Wuding chickens. These results suggest that the GH part of the somatotropic axis is the main regulator of growth rate, while IGF-1 may regulate both growth rate and body weight. Selection for growth performance and body size have altered the expression profiles of somatotropic axis genes in a breed-, age-, and tissue-specific manner, and manner, and alteration of regulatory mechanisms of these genes might play an important role in the developmental characteristics of chickens.
Liberalizing rural-to-urban construction land transfers in China : Distribution effects
Tan, Rong ; Wang, Rongyu ; Heerink, Nico - \ 2018
China Economic Review (2018). - ISSN 1043-951X
China - Distribution - Land market - Tradable quotas
China's land market is characterized by a dual urban-rural system, with the government in control of rural-urban land transfers. In recent years, different types of pilot projects have been implemented to experiment with liberalizing markets for rural-urban construction land transfers. The objective of this study is to gain insights into the distributional effects of three different types of land liberalization rules by making a comparative analysis of three pilot projects carried out under each of these liberalization rules. We find that transfers facing more liberalized rules result in higher shares of land revenue flowing to the rural sector and thereby reduce the ruralurban income gap. But direct transfers between rural and urban land users also contribute to growing income inequality within the rural sector, as households living in urban fringes benefit relatively more from such transfers. A tradable quota system can reduce the impact of location on the price of land, and thereby contribute to a more equal distribution of the revenues of rural-urban land transfers within the rural sector.
Effect of vegan fecal microbiota transplantation on carnitine- and choline-derived trimethylamine-N-oxide production and vascular inflammation in patients with metabolic syndrome
Smits, Loek P. ; Kootte, Ruud S. ; Levin, Evgeni ; Prodan, Andrei ; Fuentes, Susana ; Zoetendal, Erwin G. ; Wang, Zeneng ; Levison, Bruce S. ; Cleophas, Maartje C.P. ; Kemper, E.M. ; Dallinga-Thie, Geesje M. ; Groen, Albert K. ; Joosten, Leo A.B. ; Netea, Mihai G. ; Stroes, Erik S.G. ; Vos, Willem M. de; Hazen, Stanley L. ; Nieuwdorp, Max - \ 2018
Journal of the American Heart Association 7 (2018)7. - ISSN 2047-9980
Atherosclerosis - Cardiovascular disease - Cardiovascular imaging - Inflammation - Metabolism
Background--Intestinal microbiota have been found to be linked to cardiovascular disease via conversion of the dietary compounds choline and carnitine to the atherogenic metabolite TMAO (trimethylamine-N-oxide). Specifically, a vegan diet was associated with decreased plasma TMAO levels and nearly absent TMAO production on carnitine challenge. Methods and Results--We performed a double-blind randomized controlled pilot study in which 20 male metabolic syndrome patients were randomized to single lean vegan-donor or autologous fecal microbiota transplantation. At baseline and 2 weeks thereafter, we determined the ability to produce TMAO from d6-choline and d3-carnitine (eg, labeled and unlabeled TMAO in plasma and 24-hour urine after oral ingestion of 250 mg of both isotope-labeled precursor nutrients), and fecal samples were collected for analysis of microbiota composition. 18F-fluorodeoxyglucose positron emission tomography/computed tomography scans of the abdominal aorta, as well as ex vivo peripheral blood mononuclear cell cytokine production assays, were performed. At baseline, fecal microbiota composition differed significantly between vegans and metabolic syndrome patients. With vegan-donor fecal microbiota transplantation, intestinal microbiota composition in metabolic syndrome patients, as monitored by global fecal microbial community structure, changed toward a vegan profile in some of the patients; however, no functional effects from vegan-donor fecal microbiota transplantation were seen on TMAO production, abdominal aortic 18Ffluorodeoxyglucose uptake, or ex vivo cytokine production from peripheral blood mononuclear cells. Conclusions--Single lean vegan-donor fecal microbiota transplantation in metabolic syndrome patients resulted in detectable changes in intestinal microbiota composition but failed to elicit changes in TMAO production capacity or parameters related to vascular inflammation.
A Pressure Test to Make 10 Molecules in 90 Days : External Evaluation of Methods to Engineer Biology
Casini, Arturo ; Chang, Fang Yuan ; Eluere, Raissa ; King, Andrew M. ; Young, Eric M. ; Dudley, Quentin M. ; Karim, Ashty ; Pratt, Katelin ; Bristol, Cassandra ; Forget, Anthony ; Ghodasara, Amar ; Warden-Rothman, Robert ; Gan, Rui ; Cristofaro, Alexander ; Borujeni, Amin Espah ; Ryu, Min Hyung ; Li, Jian ; Kwon, Yong Chan ; Wang, He ; Tatsis, Evangelos ; Rodriguez-Lopez, Carlos ; O'Connor, Sarah ; Medema, Marnix H. ; Fischbach, Michael A. ; Jewett, Michael C. ; Voigt, Christopher ; Gordon, D.B. - \ 2018
Journal of the American Chemical Society 140 (2018)12. - ISSN 0002-7863 - p. 4302 - 4316.
Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species (Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.
Effects of natural organic matter with different properties on levofloxacin adsorption to goethite : Experiments and modeling
Qin, Xiaopeng ; Du, Ping ; Chen, Juan ; Liu, Fei ; Wang, Guangcai ; Weng, Liping - \ 2018
Chemical Engineering Journal 345 (2018). - ISSN 1385-8947 - p. 425 - 431.
Fluoroquinolone - Fulvic acid - Goethite - Humic acid - Hydrophobic interactions - Specific ultraviolet absorbance
Adsorption of levofloxacin (LEV) to goethite in the pH range of 3–10, and in the absence or presence of natural organic matter (NOM) represented by nine types of humic acid (HA) and fulvic acid (FA), was studied using batch experiments. The adsorption of LEV to goethite was weak and showed a maximum around pH 5.8. Adding NOM to goethite strongly increased LEV adsorption to goethite, but hardly affected its pH dependency. The adsorption envelopes were well fitted to a linear additive model, in which LEV adsorption to goethite was simulated with the Charge Distribution Multi-Site Complexation (CD-MUSIC) model, and LEV adsorption to NOM was simulated with the Langmuir model. The fitted affinity constants (log K) for LEV adsorption to NOM were significantly and positively correlated with the SUVA (specific ultraviolet absorbance at 280 nm) values of NOM, and negatively correlated with E2/E3 (absorbance ratio at 250 nm and 365 nm) values, carboxyl contents, and the polarity of NOM. The results indicated that aromatic moieties of NOM play a key role in the interactions between LEV and NOM, and hydrophobic interactions and π-π interactions were the major mechanisms for LEV adsorption to NOM, whereas H-bond or surface complexation might not play an important role. Results show that both the concentrations and properties of NOM have a significant effect on the distribution or treatment of antibiotics in soils and waters, which will eventually affect the influence of antibiotics on microorganisms in the environmental systems.
Hotspots for nitrogen and phosphorus losses to waters from food production in China
Wang, M. ; Ma, L. ; Strokal, M. ; Kroeze, C. - \ 2018
Hotspots for nitrogen and phosphorus losses from food production to waters in China
Wang, M. ; Ma, L. ; Strokal, M. ; Kroeze, Carolien - \ 2018
Geophysical Research Abstracts 20 (2018). - ISSN 1029-7006 - 1 p.
abstract
A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans
Razeq, Fakhria M. ; Jurak, Edita ; Stogios, Peter J. ; Yan, Ruoyu ; Tenkanen, Maija ; Kabel, Mirjam A. ; Wang, Weijun ; Master, Emma R. - \ 2018
Biotechnology for Biofuels 11 (2018)1. - ISSN 1754-6834
Acetyl xylan esterase - Glucuronic acid - Polysaccharide utilization loci - SGNH hydrolase - Xylan - α-Glucuronidase
Background: Acetylated 4-O-(methyl)glucuronoxylan (GX) is the main hemicellulose in deciduous hardwood, and comprises a β-(1→4)-linked xylopyranosyl (Xylp) backbone substituted by both acetyl groups and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Whereas enzymes that target singly acetylated Xylp or doubly 2,3-O-acetyl-Xylp have been well characterized, those targeting (2-O-MeGlcpA)3-O-acetyl-Xylp structures in glucuronoxylan have remained elusive. Results: An unclassified carbohydrate esterase (FjoAcXE) was identified as a protein of unknown function from a polysaccharide utilization locus (PUL) otherwise comprising carbohydrate-active enzyme families known to target xylan. FjoAcXE was shown to efficiently release acetyl groups from internal (2-O-MeGlcpA)3-O-acetyl-Xylp structures, an activity that has been sought after but lacking in known carbohydrate esterases. FjoAcXE action boosted the activity of α-glucuronidases from families GH67 and GH115 by five and nine times, respectively. Moreover, FjoAcXE activity was not only restricted to GX, but also deacetylated (3-O-Araf)2-O-acetyl-Xylp of feruloylated xylooligomers, confirming the broad substrate range of this new carbohydrate esterase. Conclusion: This study reports the discovery and characterization of the novel carbohydrate esterase, FjoAcXE. In addition to cleaving singly acetylated Xylp, and doubly 2,3-O-acetyl-Xylp, FjoAcXE efficiently cleaves internal 3-O-acetyl-Xylp linkages in (2-O-MeGlcpA)3-O-acetyl-Xylp residues along with densely substituted and branched xylooligomers; activities that until now were missing from the arsenal of enzymes required for xylan conversion.
Allopolyploidization in Cucumis contributes to delayed leaf maturation with repression of redundant homoeologous genes
Yu, Xiaqing ; Wang, Xixi ; Hyldgaard, Benita ; Zhu, Zaobing ; Zhou, Rong ; Kjaer, Katrine Heinsvig ; Ouzounis, Theoharis ; Lou, Qunfeng ; Li, Ji ; Cai, Qingsheng ; Rosenqvist, Eva ; Ottosen, Carl-Otto ; Chen, Jinfeng - \ 2018
The Plant Journal 94 (2018). - ISSN 0960-7412 - p. 393 - 404.
The important role of polyploidy in plant evolution is widely recognized. However, many questions remain to be explored to address how polyploidy affects the phenotype of the plant. To shed light on the phenotypic and molecular impacts of allopolyploidy, we investigated the leaf development of a synthesized allotetraploid (Cucumis × hytivus), with an emphasis on chlorophyll development. Delayed leaf maturation was identified in C. × hytivus, based on delayed leaf expansion, initial chlorophyll deficiency in the leaves and disordered sink‐source transition. Anatomical observations also revealed disturbed chloroplast development in C. ×hytivus. The determination of chlorophyll biosynthesis intermediates suggested that the chlorophyll biosynthesis pathway of C. × hytivus is blocked at the site at which uroporphyrinogen III is catalysed to coproporphyrinogen III. Three chlorophyll biosynthesis‐related genes, HEMA1, HEME2 and POR, were significantly repressed in C. × hytivus. Sequence alignment showed both synonymous and non‐synonymous substitutions in the HEMA1, HEME2 and POR genes of the parents. Cloning of the chlorophyll biosynthetic genes suggested the retention of homoeologs. In addition, a chimeric clone of the HEMA1 gene that consisted of homologous genes from the parents was identified in C. × hytivus. Overall, our results showed that allopolyploidization in Cucumis has resulted in disturbed chloroplast development and reduced chlorophyll biosynthesis caused by the repressed expression of duplicated homologous genes, which further led to delayed leaf maturation in the allotetraploid, C. × hytivus. The preferential retention/loss of certain types of genes and non‐reciprocal homoeologous recombination were also supported in the present study, which provides new insights into the impact of allopolyploidy.
Assessing stakeholder needs for adaptation tracking
Wang, Frances M. ; Ford, James D. ; Lesnikowski, Alexandra C. ; Chen, Chen ; Berrang-Ford, L. ; Biesbroek, G.R. ; Heymann, Jody ; Grecequet, Martina ; Huq, Saleemul - \ 2018
In: Adaptation Metrics / Christiansen, L., Martinezz, D., Naswa , P., Copenhagen, Denmark : UNEP DTU Partnership (UNEP-DTU perspectives Series 1) - ISBN 9788793458277 - p. 49 - 61.
Arbuscular mycorrhizal fungi negatively affect nitrogen acquisition and grain yield of maize in a N deficient soil
Wang, Xin Xin ; Wang, Xiaojing ; Sun, Yu ; Cheng, Yang ; Liu, Shitong ; Chen, Xinping ; Feng, Gu ; Kuyper, Thomas W. - \ 2018
Frontiers in Microbiology 9 (2018)MAR. - ISSN 1664-302X
Arbuscular mycorrhizal fungi - Benomyl - Competition - Maize - Nitrogen uptake
Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the acquisition of immobile nutrients, particularly phosphorus. However, because nitrogen (N) is more mobile in the soil solution and easier to access by plants roots, the role of AMF in enhancing N acquisition is regarded as less important for host plants. Because AMF have a substantial N demand, competition for N between AMF and plants particularly under low N condition is possible. Thus, it is necessary to know whether or not AMF affect N uptake of plants and thereby affect plant growth under field conditions. We conducted a 2-year field trial and pot experiments in a greenhouse by using benomyl to suppress colonization of maize roots by indigenous AMF at both low and high N application rates. Benomyl reduced mycorrhizal colonization of maize plants in all experiments. Benomyl-treated maize had a higher shoot N concentration and content and produced more grain under field conditions. Greenhouse pot experiments showed that benomyl also enhanced maize growth and N concentration and N content when the soil was not sterilized, but had no effect on maize biomass and N content when the soil was sterilized but a microbial wash added, providing evidence that increased plant performance is at least partly caused by direct effects of benomyl on AMF. We conclude that AMF can reduce N acquisition and thereby reduce grain yield of maize in N-limiting soils.
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