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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Poor vitamin d status in active pulmonary tuberculosis patients and its correlation with leptin and tnf-α
Wang, Qiuzhen ; Ma, Aiguo ; Gao, Tianlin ; Liu, Yufeng ; Ren, Lisheng ; Han, Lei ; Wei, Boyang ; Liu, Qian ; Dong, Chunjiang ; Mu, Yuze ; Li, Duo ; Kok, Frans J. ; Schouten, Evert G. - \ 2019
Journal of Nutritional Science and Vitaminology 65 (2019)5. - ISSN 0301-4800 - p. 390 - 398.
Co-morbidity - Diabetes - Immune activity - Inflammatory markers - Leptin - Serum 25(OH)D - TNF-α - Tuberculosis

Summary Vitamin D deficiency (VDD) is common in tuberculosis (TB) and may be implicated in the etiology of the disease and in its clinical course. The aim of this study was to investigate the association between leptin, inflammatory markers and VD status in TB patients, stratified for presence or absence of diabetes mellitus (DM). Two hundred ninety-nine TB patients were recruited from October 2015 to August 2016. Also, 91 normal controls were included. The information including socio-demographics, dietary intake and living habits was obtained by face-to-face interview. Serum concentrations of leptin and TNF-α, CRP and IL-6 were compared between TB patients with and without severe VDD (SVDD). Pearson’s correlation was used to analyze the association between TNF-α, leptin and 25-hydroxyvitamin D (25(OH)D). A significantly higher prevalence of VDD and SVDD was observed in TB patients compared with normal controls (93.0% vs 70.3%, 65.9% vs 3.3% respectively). Concentration of leptin was significantly lower, while TNF-α higher in TB patients with SVDD compared to those without (p<0.05). After adjustment for con-founders, leptin was positively associated with 25(OH)D (r=0.210, p=0.002) with similar correlation in TB patients with DM (r=0.240, p=0.020). A negative association between TNF-α and 25(OH)D was observed (r=-0.197, p=0.003), which was significant only in the subgroup without DM (r=-0.304, p=0.001). Our findings indicate that a higher VD status in TB patients may be related to higher immune activity and less serious tissue damage, and that this relation is different according to presence or absence of DM co-morbidity.

Genetic variation associated with Alpha-synuclein pathology in Caenorhabditis elegans
Wang, Yiru A. - \ 2019
Wageningen University. Promotor(en): J.E. Kammenga, co-promotor(en): M.G. Sterken; S.C. Harvey. - Wageningen : Wageningen University - ISBN 9789463951517 - 144
Nonlinear responses of soil nematode community composition to increasing aridity
Xiong, Dan ; Wei, Cun Zheng ; Wubs, Jasper E.R. ; Veen, G.J. ; Liang, Wenju ; Wang, Xiaobo ; Li, Qi ; Putten, Wim H. Van der; Han, Xingguo - \ 2019
Global Ecology and Biogeography (2019). - ISSN 1466-822X
aridity - biodiversity - global climate change - grassland transect - nonlinear response - soil nematode community

Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have a poor understanding of how belowground communities respond. In order to understand the longer term responses of different trophic levels in the soil food web to increasing aridity, we investigated the abundance, richness and community similarity of the soil nematode community along a 3,200 km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from.43 to.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used generalized additive (mixed) models to analyse the abundance, richness and community similarity patterns of soil nematodes. We used structural equation modelling (SEM) to disentangle the direct and indirect environmental drivers (aridity, soil and plant variables) of the nematode community. Results: The abundance, richness and similarity of nematode communities declined nonlinearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred in arid conditions (aridity >.80). However, the shape of the response to aridity differed among nematode feeding groups. In arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than for fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but instead were affected directly by aridity. Main conclusions: Our results showed that in mesic grasslands, increasing aridity primarily caused a decline in nematode abundance, whereas increasing aridity in xeric grasslands led to a loss of nematode diversity. The nonlinear responses of nematodes to aridity could also result in nonlinear shifts in ecosystem functioning, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.

The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

Food allergy : From molecular mechanisms to control strategies
Fu, Linglin ; Cherayil, Bobby J. ; Shi, Haining ; Wang, Yanbo ; Zhu, Yang - \ 2019
Springer Nature Singapore - ISBN 9789811369278 - 214 p.

This book addresses the molecular mechanisms of food allergies and related control strategies. To do so, it covers a broad range of topics, including: the basic immunology of food allergies, including crosstalk between gut mucosal immunity and allergens; types of food allergens, structure of food allergen epitopes and cross-reactivity; detection and quantification methods for food allergens; in vitro and in vivo models for evaluating allergenicity; novel food processing methods for the development of hypoallergenic foods; bioactive natural compounds and functional foods for alleviating allergic reactions; modulation of the microbiota in food allergies and use of probiotics in allergic response regulation; and risk assessment and control strategies for food allergens. The information provided will enable food scientists/specialists to design safer and more functional food products, and will help regulatory agencies identify and label food allergens (and thus help consumers avoid allergic reactions). It will help clinicians and public health investigators prevent or treat outbreaks of food allergies, and will provide food producers and processors, as well as government inspectors, with valuable insights into evaluation, risk assessment and control strategies for allergens. Lastly, it will benefit upper-level undergraduate and graduate students in food science and safety, public health, medicine, nutrition and related fields.

Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking
Sikdar, Sinjini ; Joehanes, Roby ; Joubert, Bonnie R. ; Xu, Cheng Jian ; Vives-Usano, Marta ; Rezwan, Faisal I. ; Felix, Janine F. ; Ward, James M. ; Guan, Weihua ; Richmond, Rebecca C. ; Brody, Jennifer A. ; Küpers, Leanne K. ; Baïz, Nour ; Håberg, Siri E. ; Smith, Jennifer A. ; Reese, Sarah E. ; Aslibekyan, Stella ; Hoyo, Cathrine ; Dhingra, Radhika ; Markunas, Christina A. ; Xu, Tao ; Reynolds, Lindsay M. ; Just, Allan C. ; Mandaviya, Pooja R. ; Ghantous, Akram ; Bennett, Brian D. ; Wang, Tianyuan ; Consortium, The Bios ; Bakulski, Kelly M. ; Melen, Erik ; Zhao, Shanshan ; Jin, Jianping ; Herceg, Zdenko ; Meurs, Joyce Van; Taylor, Jack A. ; Baccarelli, Andrea A. ; Murphy, Susan K. ; Liu, Yongmei ; Munthe-Kaas, Monica Cheng ; Deary, Ian J. ; Nystad, Wenche ; Waldenberger, Melanie ; Annesi-Maesano, Isabella ; Conneely, Karen ; Jaddoe, Vincent W.V. ; Arnett, Donna ; Snieder, Harold ; Kardia, Sharon L.R. ; Relton, Caroline L. ; Ong, Ken K. ; Ewart, Susan ; Moreno-Macias, Hortensia ; Romieu, Isabelle ; Sotoodehnia, Nona ; Fornage, Myriam ; Motsinger-Reif, Alison ; Koppelman, Gerard H. ; Bustamante, Mariona ; Levy, Daniel ; London, Stephanie J. - \ 2019
Epigenomics 11 (2019)13. - ISSN 1750-1911 - p. 1487 - 1500.
cigarette smoking - epigenetics - infant - maternal exposure - methylation

Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.

Forest connectivity, host assemblage characteristics of local and neighboring counties, and temperature jointly shape the spatial expansion of lyme disease in United States
Wang, Yingying X.G. ; Matson, Kevin D. ; Xu, Yanjie ; Prins, Herbert H.T. ; Huang, Zheng Y.X. ; Boer, Willem F. de - \ 2019
Remote Sensing 11 (2019)20. - ISSN 2072-4292
Assemblage similarity - Disease spread - Forest cover - Host assemblage composition - Infection intensity

Understanding risk factors for the spread of infectious diseases over time and across the landscape is critical for managing disease risk. While habitat connectivity and characteristics of local and neighboring animal (i.e., host) assemblages are known to influence the spread of diseases, the interactions among these factors remain poorly understood. In this study, we conducted a county-level analysis to test the effects of forest connectivity, together with the suitability of local assemblage (measured by the similarity of local host assemblage with neighboring assemblages) and the infection intensity of neighboring counties on the spatial expansion of Lyme disease in the United States. Our results suggested that both the similarity of local host assemblage and the infection intensity of neighboring counties were positively correlated with the probability of disease spread. Moreover, we found that increasing forest connectivity could facilitate the positive effect of neighbor infection intensity. In contrast, the effect size of the host assemblage similarity decreased with increasing connectivity, suggesting that host assemblage similarity was less effective in well-connected habitats. Our results thus indicate that habitat connectivity can indirectly influence disease spread by mediating the effects of other risk factors.

Mito-docking: A Novel In Vivo Method to Detect Protein–Protein Interactions
Shao, Wei ; He, Lihong ; Deng, Fei ; Wang, Hualin ; Vlak, Just M. ; Hu, Zhihong ; Wang, Manli - \ 2019
Small Methods 3 (2019)10. - ISSN 2366-9608
in vivo - method - Mito-docking - nuclear import - protein–protein interactions

Many methods have been developed to detect protein–protein interactions (PPIs) and explore cellular processes. However, effective methods for detecting complicated PPIs under physical conditions are still in demand. Here, a simple and efficient mitochondria-docking (Mito-docking) method for PPI detection in vivo is developed. The strategy is to anchor a “bait” protein to mitochondrial outer membrane (MOM), and then trap the “prey” protein onto MOM. In this way, interacting signals are enriched to allow easy detection. This method efficiently detects the well-known interaction between two G protein subunits (Gγ2 with Gβ1) and is successfully applied to investigate the recognition of importin α superfamily members for the classical nuclear localization signal (NLS) of simian virus 40 (SV40) large T antigen, which are highly dynamic and not easily visualized by conventional methods. As far as is known, this is the first time that the interaction between human importin α receptors with NLSs has been visualized. The results prove that Mito-docking can be used as a simple, straightforward, and intuitive method to study PPIs qualitatively and quantitatively in vivo.

Recently duplicated sesterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota.
Chen, Qingwen ; Jiang, Ting ; Liu, Yong-Xiu ; Haili, Liu ; Zhao, T. ; Liu, Zhixi ; Gan, Xiangchao ; Hallab, Asis ; Wang, Xuemei ; He, Juan ; Ma, Yihua ; Zhang, Fengxia ; Jin, Tao ; Schranz, M.E. ; Wang, Yong ; Yang, Bai - \ 2019
Science in China Series C-Life Sciences 62 (2019)7. - ISSN 1006-9305 - p. 947 - 958.
Some species are more equal than others: phylogenetic relatedness predicts disease pressure
Wang, Yingying - \ 2019
Wageningen University. Promotor(en): H.H.T. Prins; W.F. de Boer, co-promotor(en): K.D. Matson. - Wageningen : Wageningen University - ISBN 9789463950961 - 151
Loss of functional connectivity in migration networks induces population decline in migratory birds
Xu, Yanjie ; Si, Yali ; Wang, Yingying ; Zhang, Yong ; Prins, Herbert H.T. ; Cao, Lei ; Boer, Willem F. de - \ 2019
Ecological Applications 29 (2019)7. - ISSN 1051-0761 - p. e01960 - e01960.
bird migration - habitat loss - life history - network robustness - population dynamics - species traits - wetland

Migratory birds rely on a habitat network along their migration routes by temporarily occupying stopover sites between breeding and non-breeding grounds. Removal or degradation of stopover sites in a network might impede movement and thereby reduce migration success and survival. The extent to which the breakdown of migration networks, due to changes in land use, impacts the population sizes of migratory birds is poorly understood. We measured the functional connectivity of migration networks of waterfowl species that migrate over the East Asian-Australasian Flyway from 1992 to 2015. We analysed the relationship between changes in non-breeding population sizes and changes in functional connectivity, while taking into account other commonly considered species traits, using a phylogenetic linear mixed model. We found that population sizes significantly declined with a reduction in the functional connectivity of migration networks; no other variables were important. We conclude that the current decrease in functional connectivity, due to habitat loss and degradation in migration networks, can negatively and crucially impact population sizes of migratory birds. Our findings provide new insights into the underlying mechanisms that affect population trends of migratory birds under environmental changes. Establishment of international agreements leading to the creation of systematic conservation networks associated with migratory species' distributions and stopover sites may safeguard migratory bird populations.

Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

De novo transcriptome analysis of Viola × wittrockiana exposed to high temperature stress
Du, Xiaohua ; Zhu, Xiaopei ; Yang, Yaping ; Wang, Yanli ; Arens, Paul ; Liu, Huichao - \ 2019
PLoS ONE 14 (2019)9. - ISSN 1932-6203

Around the world, pansies are one of the most popular garden flowers, but they are generally sensitive to high temperatures, and this limits the practicality of planting them during the warmest days of the year. However, a few pansy germplasms with improved heat tolerance have been discovered or bred, but the mechanisms of their heat resistance are not understood. In this study, we investigated the transcript profiles of a heat-tolerant pansy inbred line, DFM16, in response to high temperatures using RNAseq. Approximately 55.48 Gb of nucleotide data were obtained and assembled into 167,576 unigenes with an average length of 959 bp, of which, 5,708 genes were found to be differentially expressed after heat treatments. Real-time qPCR was performed to validate the expression profiles of the selected genes. Nine metabolic pathways were found to be significantly enriched, in the analysis of the differentially expressed genes. Several potentially interesting genes that encoded putative transcription regulators or key components involving heat shock protein (HSP), heat shock transcription factors (HSF), and antioxidants biosynthesis, were identified. These genes were highlighted to indicate their significance in response to heat stress and will be used as candidate genes to improve pansy heat-tolerance in the future.

Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing
Zwart, Mark P. ; Ali, Ghulam ; Strien, Elisabeth A. van; Schijlen, Elio G.W.M. ; Wang, Manli ; Werf, Wopke van der; Vlak, Just M. - \ 2019
Viruses 11 (2019)9. - ISSN 1999-4915
deep sequencing - genomics - Illumina - SpltNPV - Spodoptera litura nucleopolyhedrovirus - virulence

Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.

Selection and gene flow shape niche-associated variation in pheromone response
Lee, Daehan ; Zdraljevic, Stefan ; Cook, Daniel E. ; Frézal, Lise ; Hsu, Jung-Chen ; Sterken, Mark G. ; Riksen, Joost A.G. ; Wang, John ; Kammenga, Jan E. ; Braendle, Christian ; Félix, Marie-Anne ; Schroeder, Frank C. ; Andersen, Erik C. - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1455 - 1463.
From quorum sensing in bacteria to pheromone signalling in social insects, chemical communication mediates interactions among individuals in local populations. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density; high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were previously shown to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world; this deletion underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbour individuals with a wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating the migration of species and providing a favourable niche for the recently arisen srg-37 deletion.

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

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

Water for maize for pigs for pork: An analysis of inter-provincial trade in China
Zhuo, La ; Liu, Yilin ; Yang, Hong ; Hoekstra, Arjen Y. ; Liu, Wenfeng ; Cao, Xinchun ; Wang, Mengru ; Wu, Pute - \ 2019
Water Research 166 (2019). - ISSN 0043-1354
Maize - Pork - Supply chain - Virtual water trade - Water footprint

Trade in commodities implies trade in virtual water (VW), which refers to the water that was used to produce the traded goods. Various studies have quantified international or inter-provincial virtual water (VW) flows related to the trade in crops and animal products. Until date, however, no effort has been undertaken to understand how the water embodied in traded feed crops (trade stage TS1) will be transferred further because of trade in animal products (trade stage TS2). This is the first study showing this mechanism, in a case study in China for maize (the major pig feed) and pork (the dominant meat), considering the period 2000–2013. We estimate the annual green and blue water footprints in maize production and then quantify the inter-provincial VW flows related to trade in maize (TS1) and trade in maize embodied in pork (TS2). Results show that in TS1, maize-related VW flowed from the water-scarce North to the water-rich South, with an increase of 40% over the study period (from 43 to 61 billion m3 y−1). In TS2, about 10% of the water embodied in maize exports from North to South China returns in the form of pork, with an increase in the absolute amount of 25% (from 4.8 to 6.1 billion m3 y−1). Considering blue VW flows specifically, we find that North-to-South blue VW flows decreased by 5% in TS1, while South-to-North blue VW flows increased by 23% in TS2.

FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum
Kong, Xiangjiu ; Zhang, Hao ; Wang, Xiaoliang ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Brankovics, Balázs ; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH- 1 and 1FgPex3 knock-out strains. The GFP and RFP transformants in the 1FgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The 1FgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid b-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the 1FgPex3 mutant was sensitive to osmotic stressors
as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of 1FgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
Exploring near-surface ground ice distribution in patterned-ground tundracorrelations with topography, soil and vegetation: correlations with topography, soil and vegetation
Wang, Peng ; Jager, Judith de; Nauta, Ake ; Huissteden, Jacobus van; Trofim, Maximov C. ; Limpens, Juul - \ 2019
Plant and Soil (2019). - ISSN 0032-079X - 15 p.
Arctic tundra - Ground ice - Permafrost degradation - Polygon - Thaw depth - Vegetation

Aims: For informed predictions on the sensitivity of Arctic tundra landscape to permafrost thaw, we aimed to investigate the distribution pattern of near-surface ground ice and its influencing factors in Northeast Siberia. Methods: Near-surface permafrost cores (60 cm) were sampled along small-scale topographic gradients in two drained lakebeds. We investigated which factors (vegetation, hydrological and soil) correlated strongest with ice content and explored its spatial heterogeneity at different scales (1 to 100 m). Results: The ice content was highest in the depressions of the wet lakebed and lowest at the slopes of the dry lakebed. In the wet lakebed the ice content increased with depth, while in the dry lakebed the vertical distribution depended on topographical position. Spatial variability in ice content was similar at different scales, stressing strong influence of local drivers. 0–60 cm ice content correlated strongest with soil moisture of the overlying unfrozen soil, while 0–20 cm ice content correlated strongest with vegetation characteristics. Conclusions: Our study implies that vegetation effect on microclimate is strong enough to affect near-surface ice distribution, and that ice-rich tundra may be highly sensitive to thaw once climate warming offsets the protective impact of vegetation.

Enlightening force chains: a review of photoelasticimetry in granular matter
Abed Zadeh, Aghil ; Barés, Jonathan ; Brzinski, Theodore A. ; Daniels, Karen E. ; Dijksman, Joshua ; Docquier, Nicolas ; Everitt, Henry O. ; Kollmer, Jonathan E. ; Lantsoght, Olivier ; Wang, Dong ; Workamp, Marcel ; Zhao, Yiqiu ; Zheng, Hu - \ 2019
Granular Matter 21 (2019). - ISSN 1434-5021
Experimental methods - Force chains - Image post-processing - Photoelasticimetry - Protocols

A photoelastic material will reveal its internal stresses when observed through polarizing filters. This eye-catching property has enlightened our understanding of granular materials for over half a century, whether in the service of art, education, or scientific research. In this review article in honor of Robert Behringer, we highlight both his pioneering use of the method in physics research, and its reach into the public sphere through museum exhibits and outreach programs. We aim to provide clear protocols for artists, exhibit-designers, educators, and scientists to use in their own endeavors. It is our hope that this will build awareness about the ubiquitous presence of granular matter in our lives, enlighten its puzzling behavior, and promote conversations about its importance in environmental and industrial contexts. To aid in this endeavor, this paper also serves as a front door to a detailed wiki containing open, community-curated guidance on putting these methods into practice (Abed-Zadeh et al. in Photoelastic methods wiki, 2019).

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