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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Optimized sowing time windows mitigate climate risks for oats production under cool semi-arid growing conditions
Zhang, Yue ; Zhang, Lizhen ; Yang, Ning ; Huth, Neil ; Wang, Enli ; Werf, Wopke van der; Evers, Jochem B. ; Wang, Qi ; Zhang, Dongsheng ; Wang, Ruonan ; Gao, Hui ; Anten, Niels P.R. - \ 2019
Agricultural and Forest Meteorology 266-267 (2019). - ISSN 0168-1923 - p. 184 - 197.
APSIM-Oats - Climate change - Cumulative probability - Optimal sowing time window - Water limited potential yield - Yield gap

Year to year variability in weather poses serious risks to crop production in the environmentally fragile agro-ecosystems of cool semi-arid areas, and future climate changes might further aggravate those risks. This study aims to quantify the contribution of altered sowing time windows to reduce climate risk for the production of oats (Avena sativa), a crop that is well adapted to short growing seasons and low rainfall. The APSIM-Oats model was calibrated and validated for phenology, above-ground dry matter and yield using data from field experiments with five sowing dates, conducted from 2009 to 2013 in Inner Mongolia, China. The model was used to determine yield trends and yield-limiting factors under rain-fed conditions using historical weather data. Changes in temperature had greater impact on crop production than changes in rainfall and the simulations indicated the importance of changed sowing windows to lengthen the growth duration and optimize water use. Delayed sowing of oats, 10 days later than current practice, ensured more secure temperature and rainfall conditions from emergence to flowering and substantially increased yields and decreased climate risk. Delayed sowing also reduced climate risk under two future climate scenarios, RCP4.5 (stabilize growth) and RCP8.5 (high greenhouse gas emission). We conclude that adaptation of sowing time of oats provides a practical strategy for enhancing yield and mitigating climate risk under climate change.

Corrigendum to ‘Revisiting the enzymatic kinetics of pepsin using isothermal titration calorimetry’
Luo, Qi ; Chen, Dongxin ; Boom, Remko M. ; Janssen, Anja E.M. - \ 2019
Food Chemistry 278 (2019). - ISSN 0308-8146 - 1 p.

The authors regret that the wrong unit was reported for the BSA solution, which should be 300 μM instead of 300 mM. It appears in two places: 1. In the paragraph after Eq. (5); 2. In the caption of Fig. 1. The authors would like to apologise for any inconvenience caused.

Which cocoa bean traits persist when eating chocolate? Real-time nosespace analysis by PTR-QiToF-MS
Acierno, Valentina ; Liu, Ningjing ; Alewijn, Martin ; Stieger, Markus ; Ruth, Saskia M. van - \ 2019
Talanta 195 (2019). - ISSN 0039-9140 - p. 676 - 682.
Chocolate - Cocoa beans origin - Nosespace - PTR-QiToF-MS

More consumers have become aware of the existence of different cocoa genotypes and their origins, which resulted in a growing market of premium chocolates with single-origin beans. The question is whether traits of cocoa botanical and geographical origins still persist in the end product, especially when it is consumed. By analysing the concentrations of volatile organic compounds (VOCs) in the nose of subjects over time while they are eating, new insights about aroma release can be gained. In the current study, in vivo release of VOCs during consumption of dark chocolates with different botanical and geographical origins was examined. Proton Transfer Reaction-Quadrupole interface Time of Flight- Mass Spectrometry (PTR-Qi ToF- MS) was applied to analyse nosespace VOC profiles of 10 subjects while they were eating 10 different chocolates manufactured with beans of different botanical origins (Criollo-Forastero-Trinitario) and geographical origins (Africa-South America-Asia). The headspace of the chocolates were also analysed for comparison. Cocoa botanical information appeared to affect the nosespace profiles more than geographical information. The subjects varied considerable in their VOC release, and inter-individual differences were larger than cocoa beans differences. Nevertheless, the botanical origin was consistently reflected in the nosespace profile during eating. It was clearly possible to distinguish Criollo chocolates from the nosespace profiles despite inter-individual differences.

Identification and functional characterisation of host interactions of the potato CC-NB-LRR Rx1
Sukarta, O.C.A. ; Slootweg, E.J. ; Zheng, Qi ; Schoen, Ruben ; Pomp, H. ; Roosien, J. ; Smant, G. ; Goverse, A. - \ 2018
The potato Rx1 is an intracellular Nucleotide-binding Leucine Rich Repeat (NLR) immune receptor with an archetypical N-terminal coiled-coil (CC) domain. It confers extreme resistance against Potato Virus X (PVX) by gene-specific recognition of the viral coat protein (CP). Recent findings point to a role of Rx1 in the nucleus whereby it could directly bind host genetic material, though it remains unclear how this process eventually leads to defence. A possibility is that Rx1 recruits other host factors, for example via the CC domain, which is predicted to act as scaffolds for nuclear signalling. Here, we used the CC domains of Rx1 and the Rx1-like protein Gpa2 (mediates defence against the nematode Globodera pallida) as baits in a Co-IP/MS analysis after cell fractionation to co-purify putative interactors from Nicotiana benthamiana. Five hits (designated Rp01-Rp05) were further prioritized as candidate Rx1/Gpa2 interacting proteins. Similar pull-down experiments confirmed complex formation with the full-length immune receptors in plantae. Interestingly, co-expression of Rp05 alters the subcellular distribution of the Rx1-CC domain, hinting its role in Rx1-function. Transient overexpression experiments confirm that Rp05 could in fact potentiate defense against PVX. Interestingly, however, this occurs independently of Rx1. We substantiated this model by demonstrating that Rp05 could influence HR-responses by other NLR proteins (e.g. Gpa2, Sw5A/B and Mi-1) indicating that it may be a common downstream component in immune signaling. Currently, we focus on elucidating the detailed molecular underpinning of Rp05 function in R-gene mediated resistances using Rx1 as the principal model system.
Hepatic Sel1L-Hrd1 ER-Associated Degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH
Bhattacharya, Asmita ; Sun, Shengyi ; Wang, Heting ; Liu, Ming ; Long, Qiaoming ; Yin, Lei ; Kersten, A.H. ; Zhang, Kezhong ; Qi, Ling - \ 2018
GSE118658 - PRJNA486359 - Mus musculus
Fibroblast growth factor 21 (Fgf21) is a liver-derived, fasting-induced hormone with broad effects on growth, nutrient metabolism and insulin sensitivity. Here, we report the discovery of a novel mechanism regulating Fgf21 expression under growth and fasting-feeding. The Sel1LHrd1 complex is the most conserved branch of mammalian endoplasmic reticulum (ER)- associated degradation (ERAD) machinery. Mice with liver-specific deletion of Sel1L exhibit growth retardation with markedly elevated circulating Fgf21, reaching levels close to those in Fgf21 transgenic mice or pharmacological models. Mechanistically, we show that the Sel1LHrd1 ERAD complex controls Fgf21 transcription by regulating the ubiquitination and turnover (and thus nuclear abundance) of ER-resident transcription factor Crebh, while having no effect on the other well-known Fgf21 transcription factor Pparα. Our data reveal a physiologically regulated, inverse correlation between Sel1L-Hrd1 ERAD and Crebh-Fgf21 levels under fasting-feeding and growth. This study not only establishes the importance of Sel1L-Hrd1 ERAD in the liver in the regulation of systemic energy metabolism, but also reveals a novel hepatic “ERADCrebh- Fgf21” axis directly linking ER protein turnover to gene transcription and systemic metabolic regulation.
Hepatic Sel1L-Hrd1 ER-associated degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH
Bhattacharya, Asmita ; Sun, Shengyi ; Wang, Heting ; Liu, Ming ; Long, Qiaoming ; Yin, Lei ; Kersten, Sander ; Zhang, Kezhong ; Qi, Ling - \ 2018
The EMBO Journal 37 (2018)22. - ISSN 0261-4189
ER quality control - FGF21 - gene transcription - metabolism - Sel1L-Hrd1 ERAD

Fibroblast growth factor 21 (Fgf21) is a liver-derived, fasting-induced hormone with broad effects on growth, nutrient metabolism, and insulin sensitivity. Here, we report the discovery of a novel mechanism regulating Fgf21 expression under growth and fasting-feeding. The Sel1L-Hrd1 complex is the most conserved branch of mammalian endoplasmic reticulum (ER)-associated degradation (ERAD) machinery. Mice with liver-specific deletion of Sel1L exhibit growth retardation with markedly elevated circulating Fgf21, reaching levels close to those in Fgf21 transgenic mice or pharmacological models. Mechanistically, we show that the Sel1L-Hrd1 ERAD complex controls Fgf21 transcription by regulating the ubiquitination and turnover (and thus nuclear abundance) of ER-resident transcription factor Crebh, while having no effect on the other well-known Fgf21 transcription factor Pparα. Our data reveal a physiologically regulated, inverse correlation between Sel1L-Hrd1 ERAD and Crebh-Fgf21 levels under fasting-feeding and growth. This study not only establishes the importance of Sel1L-Hrd1 ERAD in the liver in the regulation of systemic energy metabolism, but also reveals a novel hepatic “ERAD-Crebh-Fgf21” axis directly linking ER protein turnover to gene transcription and systemic metabolic regulation.

Analysis and modeling of enhanced green fluorescent protein diffusivity in whey protein gels
Luo, Qi ; Sewalt, Erik ; Borst, Jan Willem ; Westphal, Adrie H. ; Boom, Remko M. ; Janssen, Anja E.M. - \ 2018
Food Research International (2018). - ISSN 0963-9969
Diffusion - FCS - Gastric digestion - GFP - Modeling - Pepsin - Whey protein gel

During gastric digestion, hydrolysis of proteins by pepsin contributes largely to the breakdown of protein-rich food. We hypothesized that the effect of pepsin is limited by its diffusivity, which is co-determined by the food structure and the local pH in the food during digestion. To investigate the principle mechanism of enzyme diffusion in food matrices, we used enhanced green fluorescent protein (EGFP) as probe to study the diffusivity of proteins in whey protein isolate gels, using fluorescence correlation spectroscopy (FCS). Gels made with different ionic strength showed distinctive elastic moduli but did not show differences in diffusivity of EGFP. Some models for diffusion in hydrogels yield good description of the obtained data, and can approximate the enzyme diffusion in diverse food matrices. However, the enzyme pepsin is more complicated than the probe EGFP, to yield more accurate predictions, electrostatic and enzyme-substrate interaction also need to be considered.

Nucleolin mediates the internalization of rabbit hemorrhagic disease virus through clathrin-dependent endocytosis
Zhu, Jie ; Miao, Qiuhong ; Tang, Jingyu ; Wang, Xiaoxue ; Dong, Dandan ; Liu, Teng ; Qi, Ruibin ; Yang, Zhibiao ; Liu, Guangqing - \ 2018
PLoS Pathogens 14 (2018)10. - ISSN 1553-7366

Rabbit hemorrhagic disease virus (RHDV) is an important member of the Caliciviridae family and a highly lethal pathogen in rabbits. Although the cell receptor of RHDV has been identified, the mechanism underlying RHDV internalization remains unknown. In this study, the entry and post-internalization of RHDV into host cells were investigated using several biochemical inhibitors and RNA interference. Our data demonstrate that rabbit nucleolin (NCL) plays a key role in RHDV internalization. Further study revealed that NCL specifically interacts with the RHDV capsid protein (VP60) through its N-terminal residues (aa 285-318), and the exact position of the VP60 protein for the interaction with NCL is located in a highly conserved region (472Asp-Val-Asn474; DVN motif). Following competitive blocking of the interaction between NCL and VP60 with an artificial DVN peptide (RRTGDVNAAAGSTNGTQ), the internalization efficiency of the virus was markedly reduced. Moreover, NCL also interacts with the C-terminal residues of clathrin light chain A, which is an important component in clathrin-dependent endocytosis. In addition, the results of animal experiments also demonstrated that artificial DVN peptides protected most rabbits from RHDV infection. These findings demonstrate that NCL is involved in RHDV internalization through clathrin-dependent endocytosis.

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 - p. e1002670 - e1002670.

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.

Macro- and micro- plastics in soil-plant system : Effects of plastic mulch film residues on wheat (Triticum aestivum) growth
Qi, Yueling ; Yang, Xiaomei ; Pelaez, Amalia Mejia ; Huerta Lwanga, Esperanza ; Beriot, Nicolas ; Gertsen, Henny ; Garbeva, Paolina ; Geissen, Violette - \ 2018
Science of the Total Environment 645 (2018). - ISSN 0048-9697 - p. 1048 - 1056.
Agroecosystem - Biodegradable mulch film - Microplastics - Plant growth - Plastic residues

Plastic residues have become a serious environmental problem in the regions with intensive use of plastic mulching. Even though plastic mulch is widely used, the effects of macro- and micro- plastic residues on the soil-plant system and the agroecosystem are largely unknown. In this study, low density polyethylene and one type of starch-based biodegradable plastic mulch film were selected and used as examples of macro- and micro- sized plastic residues. A pot experiment was performed in a climate chamber to determine what effect mixing 1% concentration of residues of these plastics with sandy soil would have on wheat growth in the presence and absence of earthworms. The results showed that macro- and micro- plastic residues affected both above-ground and below-ground parts of the wheat plant during both vegetative and reproductive growth. The type of plastic mulch films used had a strong effect on wheat growth with the biodegradable plastic mulch showing stronger negative effects as compared to polyethylene. The presence of earthworms had an overall positive effect on the wheat growth and chiefly alleviated the impairments made by plastic residues.

In vitro gastric digestion of protein-based structured food : An engineering approach
Luo, Qi - \ 2018
Wageningen University. Promotor(en): Remko Boom, co-promotor(en): Anja Janssen. - Wageningen : Wageningen University - ISBN 9789463437707 - 174
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 163 (2018)8. - ISSN 0304-8608 - p. 2295 - 2310.
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.
Dissecting Gpa2-mediated immune signalling pathways involved in resistance to the potato cyst nematode Globodera Pallida
Zheng, Qi ; Slootweg, E.J. ; Sukarta, O.C.A. ; Schaik, C.C. van; Smant, G. ; Goverse, A. - \ 2018
Mycokey round table discussions of future directions in research on chemical detection methods, genetics and biodiversity of mycotoxins
Leslie, John F. ; Lattanzio, Veronica ; Audenaert, Kris ; Battilani, Paola ; Cary, Jeffrey ; Chulze, Sofia N. ; Saeger, Sarah De; Gerardino, Annamaria ; Karlovsky, Petr ; Liao, Yu Cai ; Maragos, Chris M. ; Meca, Giuseppe ; Medina, Angel ; Moretti, Antonio ; Munkvold, Gary ; Mulè, Giuseppina ; Njobeh, Patrick ; Pecorelli, Ivan ; Perrone, Giancarlo ; Pietri, Amedeo ; Palazzini, Juan M. ; Proctor, Robert H. ; Rahayu, Endang S. ; Ramírez, Maria L. ; Samson, Robert ; Stroka, Jörg ; Sulyok, Michael ; Sumarah, Mark ; Waalwijk, Cees ; Zhang, Qi ; Zhang, Hao ; Logrieco, Antonio F. - \ 2018
Toxins 10 (2018)3. - ISSN 2072-6651
Antibodies - Biological control - Communication with non-scientists - Metabolomics - Microbiome - Multi-mycotoxin detection protocols - Nominal group discussion technique - Proteomics - Transcriptomics
MycoKey, an EU-funded Horizon 2020 project, includes a series of “Roundtable Discussions” to gather information on trending research areas in the field of mycotoxicology. This paper includes summaries of the Roundtable Discussions on Chemical Detection and Monitoring of mycotoxins and on the role of genetics and biodiversity in mycotoxin production. Discussions were managed by using the nominal group discussion technique, which generates numerous ideas and provides a ranking for those identified as the most important. Four questions were posed for each research area, as well as two questions that were common to both discussions. Test kits, usually antibody based, were one major focus of the discussions at the Chemical Detection and Monitoring roundtable because of their many favorable features, e.g., cost, speed and ease of use. The second area of focus for this roundtable was multi-mycotoxin detection protocols and the challenges still to be met to enable these protocols to become methods of choice for regulated mycotoxins. For the genetic and biodiversity group, both the depth and the breadth of trending research areas were notable. For some areas, e.g., microbiome studies, the suggested research questions were primarily of a descriptive nature. In other areas, multiple experimental approaches, e.g., transcriptomics, proteomics, RNAi and gene deletions, are needed to understand the regulation of toxin production and mechanisms underlying successful biological controls. Answers to the research questions will provide starting points for developing acceptable prevention and remediation processes. Forging a partnership between scientists and appropriately-placed communications experts was recognized by both groups as an essential step to communicating risks, while retaining overall confidence in the safety of the food supply and the integrity of the food production chain.
Spatial specificity of auxin responses coordinates wood formation
Brackmann, Klaus ; Qi, Jiyan ; Gebert, Michael ; Jouannet, Virginie ; Schlamp, Theresa ; Grünwald, Karin ; Wallner, Eva Sophie ; Novikova, Daria D. ; Levitsky, Victor G. ; Agustí, Javier ; Sanchez, Pablo ; Lohmann, Jan U. ; Greb, Thomas - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Spatial organization of signalling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signalling but its exact role and spatial organization is obscure. Here we show that, while auxin signalling levels increase in differentiating cambium descendants, a moderate level of signalling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4-expressing cells. Our results reveal an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies.
Phylogenetic classification of the world's tropical forests
Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northernhemisphere forests.

Genetically engineering Crambe abyssinica- A potentially high-value oil crop for salt land improvement
Qi, W. ; Tinnenbroek-Capel, I.E.M. ; Salentijn, E.M.J. ; Zhang, Zhao ; Huang, Bangquan ; Cheng, Jihua ; Shao, Hongbo ; Visser, R.G.F. ; Krens, F.A. ; Loo, E.N. van - \ 2018
Land Degradation and Development 29 (2018)4. - ISSN 1085-3278 - p. 1096 - 1106.
Crambe abyssinica (crambe) is a new industrial oil crop that can grow on saline soil and tolerates salty water irrigation. Genetically engineered crambe in which the seed‐oil composition is manipulated for more erucic acid and less polyunsaturated fatty acid (PUFA) would be highly beneficial to industry. In this research, lysophosphatidic acid acyltransferase 2 RNA interference (CaLPAT2‐RNAi) was introduced into the crambe genome to manipulate its oil composition. The result showed in comparison with wild type, CaLPAT2‐RNAi could significantly reduce linoleic and linolenic acid content, simultaneously increasing erucic acid content. Systematic metabolism engineering was then carried out to further study CaLPAT2‐RNAi, combined with the overexpression of Brassica napus fatty acid elongase (BnFAE), Limnanthes douglasii LPAT (LdLPAT), and RNAi of endogenous fatty acid desaturase 2 (CaFAD2‐RNAi). Oil composition analysis on the tranformants' seeds showed that (a) with CaFAD2‐RNAi, PUFA content could be dramatically decreased, in comparison with BnFAE + LdLPAT + CaFAD2‐RNAi, and BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi seeds showed lower linolenic acid content; (b) BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi could increase the erucic acid content in crambe seed oil from less than 66.6% to 71.6%, whereas the highest erucic acid content of BnFAE + LdLPAT + CaFAD2‐RNAi was 79.2%; (c) although the four‐gene combination could not increase the erucic acid content of seed oil to a higher level than the others, it led to increased carbon resource deposited into C22:1 and C18:1 moieties and lower PUFA. Summarily, the present research indicates that suppression of LPAT2 is a new, promising strategy for seed‐oil biosynthesis pathway engineering, which would increase the value of crambe oil.
Agroforestry enables high efficiency of light capture, photosynthesis and dry matter production in a semi-arid climate
Zhang, Dongsheng ; Du, Guijuan ; Sun, Zhanxiang ; Bai, Wei ; Wang, Qi ; Feng, Liangshan ; Zheng, Jiaming ; Zhang, Zhe ; Liu, Yang ; Yang, Shu ; Yang, Ning ; Feng, Chen ; Cai, Qian ; Evers, Jochem B. ; Werf, Wopke van der; Zhang, Lizhen - \ 2018
European Journal of Agronomy 94 (2018). - ISSN 1161-0301 - p. 1 - 11.
Border row effect - Leaf photosynthesis - Millet - Peanut - Sweet potato
Agroforestry systems, which combine annual crops with trees, are used widely in semi-arid regions to reduce wind erosion and improve resource (e.g. water) use efficiency. Limited knowledge is available on optimizing such systems by the choice of crop species with specific physiological traits (i.e. C3 vs C4, N-fixing vs non-N-fixing). In this study we quantified the light interception and utilization efficiency of trees and crops in agroforestry systems comprising apricot trees and a C3 species (sweet potato), a C4 species (millet) or an N-fixing legume species (peanut), and used measurements in the sole stands as a reference. A significant delay in leaf growth was found in millet. Maximum LAI of millet was 17% higher in agroforestry then expected from sole crop LAI, taking into account the relative density of 2/3, while a 25% decrease in maximum LAI compared to expected was observed in peanut and sweet potato. The total light interception in agroforestry was 54% higher than in sole tree stands and 23% higher than in sole crops. The millet intercepted more light and produced more biomass in agroforestry than peanut and sweet potato. The LUE values of the crops in the mixed systems were higher than those of the sole crops, as was the photosynthetic efficiency of individual leaves, especially in plants in the border rows of the crop strips. High light capture in agroforestry made a greater contribution to productivity of understory crops than the increases in light use efficiency. We conclude that agroforestry systems with apricot trees and annual crops, especially millet, can improve light utilization in semi-arid climates and contribute to regional sustainability and adaptation to climate change.
Nitrogen dynamics in flooded soil systems: An overview on concepts and performance of models : Model concepts of nitrogen dynamics in flooded soils
Khairudin, Nurul ; Gaydon, Donald S. ; Jing, Qi ; Zakaria, Mohamad P. ; Struik, Paul C. ; Keesman, Karel J. - \ 2018
Journal of the Science of Food and Agriculture 98 (2018)3. - ISSN 0022-5142 - p. 865 - 871.
Extensive modelling studies on nitrogen (N) dynamics in flooded soil systems have been published. Consequently, many N dynamics models are available for users to select from. With the current research trend, inclined towards multi-disciplinary research, and with substantial progress in understanding of N dynamics in flooded soil systems, the objective of this paper is to provide an overview of the modelling concepts and performance of 14 models developed to simulate N dynamics in flooded soil systems. This overview provides breadth of knowledge on the models, and, therefore, is valuable as a first step in the selection of an appropriate model for a specific application.
Current Overview of Mushroom Production in the World
Royse, Daniel J. ; Baars, J.J.P. ; Tan, Qi - \ 2017
In: Edible and Medicinal Mushrooms / Zied, Diego Cunha, Pardo-Giménez, Arturo, Wiley-Blackwell - ISBN 9781119149415
Edible, medicinal, and wild mushrooms are the three major components of the global mushroom industry. World production of cultivated, edible mushrooms has increased more than 30‐fold since 1978. China is the main producer of cultivated, edible mushrooms. Lentinus edodes is now the world's leading cultivated edible mushroom with about 22% of the world's supply. Lentinula and four other genera (Pleurotus, Auricularia, Agaricus, and Flammulina) account for 85% of the world's total supply of cultivated edible mushrooms. Beginning in about 1997, China became the world's largest producer of Flammulina velutipes. On average, consumers now enjoy about 5 kg of mushrooms per person per year. Per capita consumption is expected to continue to increase as consumers become more aware of the healthful benefits of incorporating mushrooms in their diet. Much more research is needed on the bioactive components in mushrooms to determine their biological responses in humans.
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