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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    MADS-Box Transcription Factor ZtRlm1 Is Responsible for Virulence and Development of the Fungal Wheat Pathogen Zymoseptoria tritici
    Mohammadi, Naser ; Mehrabi, Rahim ; Mirzadi Gohari, Amir ; Roostaei, Mozaffar ; Mohammadi Goltapeh, Ebrahim ; Safaie, Naser ; Kema, Gert H.J. - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    Agrobacterium tumefaciens-mediated transformation - gene deletion - pathogenicity assay - phenotyping - Zymoseptoria tritici
    Zymoseptoria tritici is one of the most economically destructive wheat diseases all over the world and is a model fungal plant pathogen within the ascomycetes. In this study, the instrumental role of the ZtRlm1 gene encoding a MADS-box transcription factor (TF) in the infection process of Z. tritici was functionally characterized as these proteins play critical roles in the global gene regulation required for various developmental and physiological processes. Our infection assays showed that ZtRlm1 mutants were attenuated in disease development as a 30 and 90% reduction in chloro-necrotic lesions and pycnidia formation, respectively, were observed in plants inoculated with ZtRlm1 mutant strains demonstrating that ZtRlm1 is a crucial factor playing a significant role in the late stage of infection corresponding with pycnidial formation. Our expression analysis demonstrated that the transcript level of ZtRlm1 is induced at 2 and 20 days post-inoculation, coinciding with pycnidial sporulation. In addition, microscopic analyses showed that branch intensity and biomass production were significantly reduced, indicating that impaired pycnidia formation is a result of impaired differentiation and biomass production in the ZtRlm1 mutants. Furthermore, melanization, a phenomenon required for fruiting body formation, was significantly hampered in ZtRlm1 mutants as they were not melanized under all tested temperature and media conditions. Overall, our data showed that impaired disease development of the ZtRlm1 mutants is mainly due to the significant impact of ZtRlm1 in different cellular processes, including differentiation, branching, fungal biomass production, and melanization, in which identification of downstream genes are of interest to increase our understanding of this pathosystem.
    The role of social capital in Iranian agricultural students' acquisition of generic skills
    Gholami, Hesamedin ; Alambeigi, Amir ; Farrokhnia, Mohammadreza ; Noroozi, Omid ; Karbasioun, Mostafa - \ 2020
    Higher Education, Skills and Work-based Learning (2020). - ISSN 2042-3896
    Agricultural graduates - Employment - Gender differences - Generic skill - Iran - Social capital

    Purpose: This study aims to investigate the role of social capital in Iranian agricultural students' acquisition of generic skills. For this purpose, the effect of various social capital dimensions on students' generic skills development was examined. Design/methodology/approach: A survey was conducted among 190 third- and fourth-year undergraduate students in one of the colleges of agriculture and natural resources in Iran. The partial least square method was used to examine the relationships among various social capital dimensions (i.e. social values, social trust, social networks, social cohesion, social participation, social communications and information sharing) with students' generic skills. Findings: The findings showed that social networks and social participation are effective factors in the generic skills development of students. A model designed for the development of students' generic skills based on their social capital level predicted up to 33% of generic skills' variances. Furthermore, the multi-group analysis showed that males and females vary on how various social capital dimensions affect their generic skills. In this respect, the social participation dimension had a significantly greater impact on female students' generic skills, whereas the generic skills of male students were influenced more by the social cohesion dimension. Practical implications: Developing generic skills through social capital can be considered as an effective strategy in countries that do not have formal programs for developing students' generic skills. Additionally, higher education policymakers should present a more supportive approach for developing generic skills of female students through social participation in the campuses. Originality/value: So far, no study has examined the relationships among various social capital dimensions and students' generic skills in Iran. The picture is even more unclear when it comes to the differences between male and female students. The results of this study confirmed the importance of social networks and social participation in the universities to support students and to improve their generic skills and, consequently, their employability competencies. Furthermore, it could be inferred that male and female students have similarities and also differences in terms of the effect of social capital on developing generic skills that can provide a path for future studies.

    Eleven grand challenges in single-cell data science
    Lähnemann, David ; Köster, Johannes ; Szczurek, Ewa ; McCarthy, Davis J. ; Hicks, Stephanie C. ; Robinson, Mark D. ; Vallejos, Catalina A. ; Campbell, Kieran R. ; Beerenwinkel, Niko ; Mahfouz, Ahmed ; Pinello, Luca ; Skums, Pavel ; Stamatakis, Alexandros ; Attolini, Camille Stephan Otto ; Aparicio, Samuel ; Baaijens, Jasmijn ; Balvert, Marleen ; Barbanson, Buys de; Cappuccio, Antonio ; Corleone, Giacomo ; Dutilh, Bas E. ; Florescu, Maria ; Guryev, Victor ; Holmer, Rens ; Jahn, Katharina ; Lobo, Thamar Jessurun ; Keizer, Emma M. ; Khatri, Indu ; Kielbasa, Szymon M. ; Korbel, Jan O. ; Kozlov, Alexey M. ; Kuo, Tzu Hao ; Lelieveldt, Boudewijn P.F. ; Mandoiu, Ion I. ; Marioni, John C. ; Marschall, Tobias ; Mölder, Felix ; Niknejad, Amir ; Raczkowski, Lukasz ; Reinders, Marcel ; Ridder, Jeroen de; Saliba, Antoine Emmanuel ; Somarakis, Antonios ; Stegle, Oliver ; Theis, Fabian J. ; Yang, Huan ; Zelikovsky, Alex ; McHardy, Alice C. ; Raphael, Benjamin J. ; Shah, Sohrab P. ; Schönhuth, Alexander - \ 2020
    Genome Biology 21 (2020)1. - ISSN 1474-7596

    The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands - or even millions - of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.

    Author Correction: Phosphopantetheinyl transferase (Ppt)-mediated biosynthesis of lysine, but not siderophores or DHN melanin, is required for virulence of Zymoseptoria tritici on wheat
    Derbyshire, Mark C. ; Gohari, Amir Mirzadi ; Mehrabi, Rahim ; Kilaru, Sreedhar ; Steinberg, Gero ; Ali, Solaf ; Bailey, Andy ; Hammond-Kosack, Kim ; Kema, Gert H.J. ; Rudd, Jason J. - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Determinants of household food waste behavior in Tehran city : A structural model
    Fami, Hossein Shabanali ; Aramyan, Lusine H. ; Sijtsema, Siet J. ; Alambaigi, Amir - \ 2019
    Resources, Conservation and Recycling 143 (2019). - ISSN 0921-3449 - p. 154 - 166.
    Consumer behavior - Food waste - Household - Tehran - Women

    About 25 million tons of food go wasted or lost in Iran which has socio-economic and environmental consequences for both the country and the households. The main objective of this research is to develop a model to examine the relationship between FCM components and the amount of FW of households in Tehran city, with a focus on urban women. By means of a structural model, this study provides a novel approach to exploring relationships between the food-related behavior of urban households and waste control (n = 1197). Besides, this study is the first attempt to quantify food waste in Iran at the household level. According to the adopted self-reporting procedure, in Tehran, every consumer wastes about 27.6 kg of edible food annually. It is found that households with better food consumption management (FCM (have a lower level of food waste. Moreover, the results have proved that other determinants such as demographic factors, economic power, information use, ability, and motivation have direct and indirect significant effects on FCM as well as on the amount of food waste generation. The findings suggest that the above-mentioned determinants are crucial and should be considered when developing a strategically sustainable food waste prevention plan.

    Rapid detection and differentiation of Salmonella species, Salmonella Typhimurium and Salmonella Enteritidis by multiplex quantitative PCR
    Heymans, Raymond ; Vila, Amir ; Heerwaarden, Caroliene A.M. van; Jansen, Claudia C.C. ; Castelijn, Greetje A.A. ; Voort, Menno van der; Biesta-Peters, Elisabeth G. - \ 2018
    PLoS ONE 13 (2018)10. - ISSN 1932-6203

    A multiplex quantitative PCR (qPCR) was developed and evaluated for the simultaneous detection of Salmonella spp., S. enterica serovar Typhimurium and S. enterica serovar Enteritidis in various (food) matrices. Early and fast detection of these pathogens facilitates effective intervention and prevents further distribution of contaminated food products on the market. Three primer and probe sets were designed to target the invA gene, the STM4200 gene, and the SEN1392 gene to detect and differentiate Salmonella spp., S. Typhimurium, and S. Enteritidis, respectively. The multiplex qPCR targeting these three genes was optimized for efficiency and linearity. By testing 225 Salmonella isolates and 34 non-Salmonella isolates from various sources the inclusivity and exclusivity were determined. The inclusivity of the multiplex qPCR was 100% for all Salmonella isolates, including 72 S. Typhimurium isolates, and 53 S. Enteritidis isolates. The exclusivity for Salmonella spp., S. Typhimurium, and S. Enteritidis was 100%, 94.6%, and 100%, respectively. No positive results were reported for non-Salmonella isolates. The limit of detection (LOD) for the qPCR was determined for the matrices poultry, minced meat, egg, herbs/spices, powdered milk, fish, animal feed, bootsocks with chicken feces and chicken down. LOD values for qPCR and the conventional culture methods were similar, except for the matrix boot-socks and down, for which the LOD for the conventional culture methods performed better than the qPCR method. In conclusion, the multiplex qPCR assay developed allows for rapid screening of Salmonella spp., S. Typhimurium, and S. Enteritidis in various (food) matrices.

    State and Capitalism in Kurdistan: Imagining Alternative futures
    Jongerden, Joost - \ 2018
    Toronto University, Amir Hassanpour Memorial Lecture, Saturday, October 13, 2018
    Erratum to: The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
    GigaScience 7 (2018)12. - ISSN 2047-217X
    Phosphopantetheinyl transferase (Ppt)-mediated biosynthesis of lysine, but not siderophores or DHN melanin, is required for virulence of Zymoseptoria tritici on wheat
    Derbyshire, Mark C. ; Gohari, Amir Mirzadi ; Mehrabi, Rahim ; Kilaru, Sreedhar ; Steinberg, Gero ; Ali, Solaf ; Bailey, Andy ; Hammond-Kosack, Kim ; Kema, Gert H.J. ; Rudd, Jason J. - \ 2018
    Scientific Reports 8 (2018)1. - ISSN 2045-2322

    Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB) disease of wheat. Z. tritici is an apoplastic fungal pathogen, which does not penetrate plant cells at any stage of infection, and has a long initial period of symptomless leaf colonisation. During this phase it is unclear to what extent the fungus can access host plant nutrients or communicate with plant cells. Several important primary and secondary metabolite pathways in fungi are regulated by the post-translational activator phosphopantetheinyl transferase (Ppt) which provides an essential co-factor for lysine biosynthesis and the activities of non-ribosomal peptide synthases (NRPS) and polyketide synthases (PKS). To investigate the relative importance of lysine biosynthesis, NRPS-based siderophore production and PKS-based DHN melanin biosynthesis, we generated deletion mutants of ZtPpt. The ∆ZtPpt strains were auxotrophic for lysine and iron, non-melanised and non-pathogenic on wheat. Deletion of the three target genes likely affected by ZtPpt loss of function (Aar- lysine; Nrps1-siderophore and Pks1- melanin), highlighted that lysine auxotrophy was the main contributing factor for loss of virulence, with no reduction caused by loss of siderophore production or melanisation. This reveals Ppt, and the lysine biosynthesis pathway, as potential targets for fungicides effective against Z. tritici.

    Water shortages worsened by reservoir effects
    Baldassarre, Giuliano Di; Wanders, Niko ; AghaKouchak, Amir ; Kuil, Linda ; Rangecroft, Sally ; Veldkamp, Ted I.E. ; Garcia, Margaret ; Oel, Pieter R. van; Breinl, Korbinian ; Loon, Anne F. van - \ 2018
    Nature Sustainability 1 (2018)11. - ISSN 2398-9629 - p. 617 - 622.

    The expansion of reservoirs to cope with droughts and water shortages is hotly debated in many places around the world. We argue that there are two counterintuitive dynamics that should be considered in this debate: supply–demand cycles and reservoir effects. Supply–demand cycles describe instances where increasing water supply enables higher water demand, which can quickly offset the initial benefits of reservoirs. Reservoir effects refer to cases where over-reliance on reservoirs increases vulnerability, and therefore increases the potential damage caused by droughts. Here we illustrate these counterintuitive dynamics with global and local examples, and discuss policy and research implications.

    The burden of cardiovascular diseases among us states, 1990-2016
    Roth, Gregory A. ; Johnson, Catherine O. ; Abate, Kalkidan Hassen ; Abd-Allah, Foad ; Ahmed, Muktar ; Alam, Khurshid ; Alam, Tahiya ; Alvis-Guzman, Nelson ; Ansari, Hossein ; Ärnlöv, Johan ; Atey, Tesfay Mehari ; Awasthi, Ashish ; Awoke, Tadesse ; Barac, Aleksandra ; Bärnighausen, Till ; Bedi, Neeraj ; Bennett, Derrick ; Bensenor, Isabela ; Biadgilign, Sibhatu ; Castañeda-Orjuela, Carlos ; Catalá-López, Ferrán ; Davletov, Kairat ; Dharmaratne, Samath ; Ding, Eric L. ; Dubey, Manisha ; Faraon, Emerito Jose Aquino ; Farid, Talha ; Farvid, Maryam S. ; Feigin, Valery ; Fernandes, João ; Frostad, Joseph ; Gebru, Alemseged ; Geleijnse, Johanna M. ; Gona, Philimon Nyakauru ; Griswold, Max ; Hailu, Gessessew Bugssa ; Hankey, Graeme J. ; Hassen, Hamid Yimam ; Havmoeller, Rasmus ; Hay, Simon ; Heckbert, Susan R. ; Irvine, Caleb Mackay Salpeter ; James, Spencer Lewis ; Jara, Dube ; Kasaeian, Amir ; Khan, Abdur Rahman ; Khera, Sahil ; Khoja, Abdullah T. ; Khubchandani, Jagdish ; Kim, Daniel ; Kolte, Dhaval ; Lal, Dharmesh ; Larsson, Anders ; Linn, Shai ; Lotufo, Paulo A. ; Razek, Hassan Magdy Abd El; Mazidi, Mohsen ; Meier, Toni ; Mendoza, Walter ; Mensah, George A. ; Meretoja, Atte ; Mezgebe, Haftay Berhane ; Mirrakhimov, Erkin ; Mohammed, Shafiu ; Moran, Andrew Edward ; Nguyen, Grant ; Nguyen, Minh ; Ong, Kanyin Liane ; Owolabi, Mayowa ; Pletcher, Martin ; Pourmalek, Farshad ; Purcell, Caroline A. ; Qorbani, Mostafa ; Rahman, Mahfuzar ; Rai, Rajesh Kumar ; Ram, Usha ; Reitsma, Marissa Bettay ; Renzaho, Andre M.N. ; Rios-Blancas, Maria Jesus ; Safiri, Saeid ; Salomon, Joshua A. ; Sartorius, Benn ; Sepanlou, Sadaf Ghajarieh ; Shaikh, Masood Ali ; Silva, Diego ; Stranges, Saverio ; Tabarés-Seisdedos, Rafael ; Atnafu, Niguse Tadele ; Thakur, J.S. ; Topor-Madry, Roman ; Truelsen, Thomas ; Tuzcu, E.M. ; Tyrovolas, Stefanos ; Ukwaja, Kingsley Nnanna ; Vasankari, Tommi ; Vlassov, Vasiliy ; Vollset, Stein Emil ; Wakayo, Tolassa ; Weintraub, Robert ; Wolfe, Charles ; Workicho, Abdulhalik ; Xu, Gelin ; Yadgir, Simon ; Yano, Yuichiro ; Yip, Paul ; Yonemoto, Naohiro ; Younis, Mustafa ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Zipkin, Ben ; Afshin, Ashkan ; Gakidou, Emmanuela ; Lim, Stephen S. ; Mokdad, Ali H. ; Naghavi, Mohsen ; Vos, Theo ; Murray, Christopher J.L. - \ 2018
    JAMA Cardiology 3 (2018)5. - ISSN 2380-6583 - p. 375 - 389.
    Importance: Cardiovascular disease (CVD) is the leading cause of death in the United States, but regional variation within the United States is large. Comparable and consistent state-level measures of total CVD burden and risk factors have not been produced previously. Objective: To quantify and describe levels and trends of lost health due to CVD within the United States from 1990 to 2016 as well as risk factors driving these changes. Design, setting, and participants: Using the Global Burden of Disease methodology, cardiovascular disease mortality, nonfatal health outcomes, and associated risk factors were analyzed by age group, sex, and year from 1990 to 2016 for all residents in the United States using standardized approaches for data processing and statistical modeling. Burden of disease was estimated for 10 groupings of CVD, and comparative risk analysis was performed. Data were analyzed from August 2016 to July 2017. Exposures: Residing in the United States. Main outcomes ans measures: Cardiovascular disease disability-Adjusted life-years (DALYs). Results: Between 1990 and 2016, age-standardized CVD DALYs for all states decreased. Several states had large rises in their relative rank ordering for total CVD DALYs among states, including Arkansas, Oklahoma, Alabama, Kentucky, Missouri, Indiana, Kansas, Alaska, and Iowa. The rate of decline varied widely across states, and CVD burden increased for a small number of states in the most recent years. Cardiovascular disease DALYs remained twice as large among men compared with women. Ischemic heart disease was the leading cause of CVD DALYs in all states, but the second most common varied by state. Trends were driven by 12 groups of risk factors, with the largest attributable CVD burden due to dietary risk exposures followed by high systolic blood pressure, high body mass index, high total cholesterol level, high fasting plasma glucose level, tobacco smoking, and low levels of physical activity. Increases in risk-deleted CVD DALY rates between 2006 and 2016 in 16 states suggest additional unmeasured risks beyond these traditional factors. Conclusions and relevance: Large disparities in total burden of CVD persist between US states despite marked improvements in CVD burden. Differences in CVD burden are largely attributable to modifiable risk exposures.
    Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance
    Kema, Gerrit H.J. ; Mirzadi Gohari, Amir ; Aouini, Lamia ; Gibriel, Hesham A.Y. ; Ware, Sarah B. ; Den Bosch, Frank van; Manning-Smith, Robbie ; Alonso-Chavez, Vasthi ; Helps, Joe ; M’Barek, Sarrah Ben; Mehrabi, Rahim ; Diaz-Trujillo, Caucasella ; Zamani, Elham ; Schouten, Henk J. ; Lee, Theo A.J. van der; Waalwijk, Cees ; Waard, Maarten A. de; Wit, Pierre J.G.M. de; Verstappen, Els C.P. ; Thomma, Bart P.H.J. ; Meijer, Harold J.G. ; Seidl, Michael F. - \ 2018
    Nature Genetics 50 (2018). - ISSN 1061-4036 - p. 375 - 380.
    Host resistance and fungicide treatments are cornerstones of plant-disease control. Here, we show that these treatments allow sex and modulate parenthood in the fungal wheat pathogen Zymoseptoria tritici. We demonstrate that the Z. tritici–wheat interaction complies with the gene-for-gene model by identifying the effector AvrStb6, which is recognized by the wheat resistance protein Stb6. Recognition triggers host resistance, thus implying removal of avirulent strains from pathogen populations. However, Z. tritici crosses on wheat show that sex occurs even with an avirulent parent, and avirulence alleles are thereby retained in subsequent populations. Crossing fungicide-sensitive and fungicide-resistant isolates under fungicide pressure results in a rapid increase in resistance-allele frequency. Isolates under selection always act as male donors, and thus disease control modulates parenthood. Modeling these observations for agricultural and natural environments reveals extended durability of host resistance and rapid emergence of fungicide resistance. Therefore, fungal sex has major implications for disease control.
    The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
    GigaScience 6 (2017)10. - ISSN 2047-217X
    16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
    The ZtVf1 transcription factor regulates development and virulence in the foliar wheat pathogen Zymoseptoria tritici
    Mohammadi, Naser ; Mehrabi, Rahim ; Mirzadi Gohari, Amir ; Mohammadi Goltapeh, Ebrahim ; Safaie, Naser ; Kema, Gert H.J. - \ 2017
    Fungal Genetics and Biology 109 (2017). - ISSN 1087-1845 - p. 26 - 35.
    Functional analysis - Fungal transformation - Gene deletion - Mycosphaerella graminicola - USER-friendly cloning
    The dimorphic fungal pathogen, Zymoseptoria tritici undergoes discrete developmental changes to complete its life cycle on wheat. Molecular mechanisms underlying morphogenesis during infection process of Z. tritici are poorly understood. In this study, we have investigated the role of ZtVf1 gene encoding a transcription factor belonging to C2-H2 subfamily. In planta assays revealed that ZtVf1 is required for virulence. Reduced necrotic lesions and low pycnidia density within the lesions resulted in significantly reduced virulence of ZtVf1 mutants. Cytological analysis showed that the impaired virulence of ZtVf1 mutants attributed to reduced penetration and colonization along with hampered pycnidia differentiation. In vitro phenotyping showed that ZtVf1 deletion affects hyphal branching and biomass production suggesting that the reduced tissue colonization by the ZtVf1 mutant might be due to lower hyphal branching and less fungal biomass production. In addition, the majority of infected substomatal cavities by the ZtVf1 mutant filled with compacted mycelia mat that did not differentiate to mature pycnidia indicating that the impaired melanization negatively affected pycnidia formation and maturation. The ZtVf1 might target multiple genes belonging to different cellular processes whose identification is of eminent interest to increase our understanding of this pathosystem. Overall, the data provided in this study indicates that attenuated pathogenicity of ZtVf1 mutant is due to involvement of this gene in the regulation of both early and late stages of infection.
    Karyotype Variability in Plant-Pathogenic Fungi
    Mehrabi, Rahim ; Mirzadi Gohari, Amir ; Kema, Gert H.J. - \ 2017
    Annual Review of Phytopathology 55 (2017). - ISSN 0066-4286 - p. 483 - 503.
    Chromosomal rearrangement - Cytological karyotyping - Electrophoretic - Evolutionary adaptation - Genome evolution - Horizontal gene transfer - Polymorphisms
    Recent advances in genetic and molecular technologies gradually paved the way for the transition from traditional fungal karyotyping to more comprehensive chromosome biology studies. Extensive chromosomal polymorphisms largely resulting from chromosomal rearrangements (CRs) are widely documented in fungal genomes. These extraordinary CRs in fungi generate substantial genome plasticity compared to other eukaryotic organisms. Here, we review the most recent findings on fungal CRs and their underlying mechanisms and discuss the functional consequences of CRs for adaptation, fungal evolution, host range, and pathogenicity of fungal plant pathogens in the context of chromosome biology. In addition to a complement of permanent chromosomes called core chromosomes, the genomes of many fungal pathogens comprise distinct unstable chromosomes called dispensable chromosomes (DCs) that also contribute to chromosome polymorphisms. Compared to the core chromosomes, the structural features of DCs usually differ for gene density, GC content, housekeeping genes, and recombination frequency. Despite their dispensability for normal growth and development, DCs have important biological roles with respect to pathogenicity in some fungi but not in others. Therefore, their evolutionary origin is also reviewed in relation to overall fungal physiology and pathogenicity.
    Reduction of Sugarcane Water Footprint by Controlled Drainage, in Khuzestan, Iran
    Jahani, Babak ; Soltani Mohammadi, Amir ; Nasseri, Abd Ali ; Oel, Pieter R. van; Sadeghi Lari, Adnan - \ 2017
    Irrigation and Drainage 66 (2017)5. - ISSN 1531-0353 - p. 884 - 895.
    Controlled drainage - Sugarcane - Water footprint - Water table management

    The main objective of this study was to estimate the different components of the water footprint for sugarcane production under the conditions of free (FD) and controlled drainage (as an on-farm strategy for agricultural water management, CD) in an arid and semi-arid region in the south-west of Iran (Khuzestan Province). The different components of the water footprint (green, blue and grey) were assessed based on on-farm measurements. The total amount of water footprint for sugarcane production in the study area stood at 250 m3t-1 in the treatment FD. Of this, 12.2, 71.8 and 16.0% were of the green, blue and grey water footprints, respectively. By using CD this value was reduced to 203 m3t-1 in total, of which, 13.7, 76.8 and 9.5% were of the green, blue and grey water footprints, respectively. This decrease in the amount of water footprint seems to be mainly a result of an increase in crop productivity (due to soil condition improvement), reduction of the in- and outflow of the sugarcane farm and also reduction of nitrate losses in the CD treatment.

    Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence
    Eves-van den Akker, Sebastian ; Laetsch, Dominik R. ; Thorpe, Peter ; Lilley, Catherine J. ; Danchin, Etienne G.J. ; Rocha, Martine Da; Rancurel, Corinne ; Holroyd, Nancy E. ; Cotton, James A. ; Szitenberg, Amir ; Grenier, Eric ; Montarry, Josselin ; Mimee, Benjamin ; Duceppe, Marc Olivier ; Boyes, Ian ; Marvin, Jessica M.C. ; Jones, Laura M. ; Yusup, Hazijah B. ; Lafond-Lapalme, Joël ; Esquibet, Magali ; Sabeh, Michael ; Rott, Michael ; Overmars, H.A. ; Finkers-Tomczak, A.M. ; Smant, G. - \ 2016
    Wageningen University & Research
    Plant-parasitic nematode - Genome sequence - Virulence - Effectors - Horizontal gene transfer
    For each gene, lists the normalized expression data for each life stage, and (if significantly differentially expressed) which expression super cluster it is grouped into.
    Burden of diarrhea in the eastern mediterranean region, 1990-2013 : Findings from the global burden of disease study 2013
    Khalil, Ibrahim ; Colombara, Danny V. ; Forouzanfar, Mohammad Hossein ; Troeger, Christopher ; Daoud, Farah ; Moradi-Lakeh, Maziar ; Bcheraoui, Charbel El; Rao, Puja C. ; Afshin, Ashkan ; Charara, Raghid ; Abate, Kalkidan Hassen ; Abd El Razek, Mohammed Magdy ; Abd-Allah, Foad ; Abu-Elyazeed, Remon ; Kiadaliri, Aliasghar Ahmad ; Akanda, Ali Shafqat ; Akseer, Nadia ; Alam, Khurshid ; Alasfoor, Deena ; Ali, Raghib ; AlMazroa, Mohammad A. ; Alomari, Mahmoud A. ; Salem Al-Raddadi, Rajaa Mohammad ; Alsharif, Ubai ; Alsowaidi, Shirina ; Altirkawi, Khalid A. ; Alvis-Guzman, Nelson ; Ammar, Walid ; Antonio, Carl Abelardo T. ; Asayesh, Hamid ; Asghar, Rana Jawad ; Atique, Suleman ; Awasthi, Ashish ; Bacha, Umar ; Badawi, Alaa ; Barac, Aleksandra ; Bedi, Neeraj ; Bekele, Tolesa ; Bensenor, Isabela M. ; Betsu, Balem Demtsu ; Bhutta, Zulfiqar ; Abdulhak, Aref A. Bin; Butt, Zahid A. ; Danawi, Hadi ; Dubey, Manisha ; Endries, Aman Yesuf ; Faghmous, Imad M.D.A. ; Farid, Talha ; Farvid, Maryam S. ; Farzadfar, Farshad ; Fereshtehnejad, Seyed Mohammad ; Fischer, Florian ; Anderson Fitchett, Joseph Robert ; Gibney, Katherine B. ; Mohamed Ginawi, Ibrahim Abdelmageem ; Gishu, Melkamu Dedefo ; Gugnani, Harish Chander ; Gupta, Rahul ; Hailu, Gessessew Bugssa ; Hamadeh, Randah Ribhi ; Hamidi, Samer ; Harb, Hilda L. ; Hedayati, Mohammad T. ; Hsairi, Mohamed ; Husseini, Abdullatif ; Jahanmehr, Nader ; Javanbakht, Mehdi ; Beyene, Tariku ; Jonas, Jost B. ; Kasaeian, Amir ; Khader, Yousef Saleh ; Khan, Abdur Rahman ; Khan, Ejaz Ahmad ; Khan, Gulfaraz ; Khoja, Tawfik Ahmed Muthafer ; Kinfu, Yohannes ; Kissoon, Niranjan ; Koyanagi, Ai ; Lal, Aparna ; Abdul Latif, Asma Abdul ; Lunevicius, Raimundas ; Abd El Razek, Hassan Magdy ; Majeed, Azeem ; Malekzadeh, Reza ; Mehari, Alem ; Mekonnen, Alemayehu B. ; Melaku, Yohannes Adama ; Memish, Ziad A. ; Mendoza, Walter ; Misganaw, Awoke ; Ibrahim Mohamed, Layla Abdalla ; Nachega, Jean B. ; Nguyen, Quyen Le ; Nisar, Muhammad Imran ; Peprah, Emmanuel Kwame ; Platts-Mills, James A. ; Pourmalek, Farshad ; Qorbani, Mostafa ; Rafay, Anwar ; Rahimi-Movaghar, Vafa ; Ur Rahman, Sajjad ; Rai, Rajesh Kumar ; Rana, Saleem M. ; Ranabhat, Chhabi L. ; Rao, Sowmya R. ; Refaat, Amany H. ; Riddle, Mark ; Roshandel, Gholamreza ; Ruhago, George Mugambage ; Saleh, Muhammad Muhammad ; Sanabria, Juan R. ; Sawhney, Monika ; Sepanlou, Sadaf G. ; Setegn, Tesfaye ; Sliwa, Karen ; Sreeramareddy, Chandrashekhar T. ; Sykes, Bryan L. ; Tavakkoli, Mohammad ; Tedla, Bemnet Amare ; Terkawi, Abdullah S. ; Ukwaja, Kingsley ; Uthman, Olalekan A. ; Westerman, Ronny ; Wubshet, Mamo ; Yenesew, Muluken A. ; Yonemoto, Naohiro ; Younis, Mustafa Z. ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Rabeeah, Abdullah A. Al; Wang, Haidong ; Naghavi, Mohsen ; Vos, Theo ; Lopez, Alan D. ; Murray, Christopher J.L. ; Mokdad, Ali H. - \ 2016
    American Journal of Tropical Medicine and Hygiene 95 (2016)6. - ISSN 0002-9637 - p. 1319 - 1329.

    Diarrheal diseases (DD) are leading causes of disease burden, death, and disability, especially in children in low-income settings. DD can also impact a child's potential livelihood through stunted physical growth, cognitive impairment, and other sequelae. As part of the Global Burden of Disease Study, we estimated DD burden, and the burden attributable to specific risk factors and particular etiologies, in the Eastern Mediterranean Region (EMR) between 1990 and 2013. For both sexes and all ages, we calculated disability-adjusted life years (DALYs), which are the sum of years of life lost and years lived with disability. We estimate that over 125,000 deaths (3.6% of total deaths) were due to DD in the EMR in 2013, with a greater burden of DD in low-and middle-income countries. Diarrhea deaths per 100,000 children under 5 years of age ranged from one (95% uncertainty interval [UI] = 0-1) in Bahrain and Oman to 471 (95% UI = 245-763) in Somalia. The pattern for diarrhea DALYs among those under 5 years of age closely followed that for diarrheal deaths. DALYs per 100,000 ranged from 739 (95% UI = 520-989) in Syria to 40,869 (95% UI = 21,540-65,823) in Somalia. Our results highlighted a highly inequitable burden of DD in EMR, mainly driven by the lack of access to proper resources such as water and sanitation. Our findings will guide preventive and treatment interventions which are based on evidence and which follow the ultimate goal of reducing the DD burden.

    Adherence of staphylococcus aureus to dyneema Purity® patches and to clinically used cardiovascular prostheses
    Basir, Amir ; Gründeman, Paul ; Moll, Frans ; Herwaarden, Joost van; Pasterkamp, Gerard ; Nijland, Reindert - \ 2016
    PLoS ONE 11 (2016)9. - ISSN 1932-6203

    Various materials that are used for vascular and heart valve prostheses carry drawbacks: some require anticoagulant drugs or have moderate durability; others are not suitable for endovascular treatment. These prostheses are associated with bacterial infections. A material potentially suitable for prostheses is Dyneema Purity®, made of ultra-high-molecularweight polyethylene. Dyneema Purity® fibers are very thin, flexible, resistant to fatigue and abrasion, and have high strength. S. aureus adherence to Dyneema Purity® was tested and compared with currently used cardiovascular prostheses. We compared adhesion of S. aureus to Dyneema Purity® (1 membrane-based and 1 yarn-composed patch) with 5 clinically used yarn-composed polyester and membrane-based expanded polytetrafluoroethylene patches. Patches were contaminated with S. aureus bacteria and bacterial adherence was quantified. S. aureus adherence was also visualized in flow conditions. Overall, bacterial adherence was higher on yarn-composed prosthesis materials, with a rough surface, than on the membrane-based materials, with a smooth surface. Adherence to Dyneema Purity® materials was non-inferior to the currently used materials. Therefore, patches of Dyneema Purity® might be attractive for use in cardiovascular applications such as catheter- based heart valves and endovascular prostheses by their good mechanical properties combined with their noninferiority regarding bacterial adhesion.

    The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the bases and regulation of parasitism and virulence
    Eves-van den Akker, Sebastian ; Laetsch, Dominik R. ; Thorpe, Peter ; Lilley, Catherine J. ; Danchin, Etienne G.J. ; Rocha, Martine Da; Rancurel, Corinne ; Holroyd, Nancy E. ; Cotton, James A. ; Szitenberg, Amir ; Overmars, H.A. ; Smant, G. - \ 2016
    A community-wide consortium was launched in 2014 to analyse the genome of Globodera rostochiensis. This devastating plant-pathogen of global economic importance is classified into pathotypes of different plant resistance-breaking phenotypes. G. rostochiensis secretes effectors from pharyngeal glands into the host to manipulate host processes and promote parasitism: some effectors were acquired by horizontal gene transfer. We have generated a draft genome assembly for G. rostochiensis to identify putative effectors and HGT events, to map gene expression through the life cycle focusing on key parasitic transitions, and to explore the genetic variation underlying eight populations including four additional plant resistance-breaking pathotypes.
    Horizontal gene transfer contributed 3.5% of the predicted genes, ~8.5% of which are deployed as effectors. We identified a putative regulatory motif consistent with the highly tissue-specific expression pattern of effectors. The six base pair DOrsal Gland motif (DOG box) is present in the promoter region of representatives from 26 of the 28 dorsal-gland effector families. Using the DOG box, we predicted a superset of putative effectors associated with this motif, validate gland cell expression for two novel genes by in situ hybridisation, and catalogue DOG effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights polymorphisms which correlate with plant resistance-breaking pathotypes.
    These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. DOG effectors are at the front line of the evolutionary arms race between plant and parasite, and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action. The G. rostochiensis consortium has rapidly established a model to study pathogenicity and virulence in plant-parasitic nematodes.
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