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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    Modulation of the Tomato Fruit Metabolome by LED Light
    Ntagkas, N. ; Vos, C.H. de; Woltering, E.J. ; Nicole, Celine ; Labrie, C.W. ; Marcelis, L.F.M. - \ 2020
    Metabolites 10 (2020)266. - ISSN 2218-1989 - 19 p.
    Metabolic profiles of tomatoes change during ripening and light can modulate the activity of relevant biochemical pathways. We investigated the effects of light directly supplied to the fruits on the metabolome of the fruit pericarp during ripening. Mature green tomatoes were exposed to well-controlled conditions with light as the only varying factor; control fruits were kept in darkness. In experiment 1 the fruits were exposed to either white light or darkness for 15 days.
    In experiment 2, fruits were exposed to different light spectra (blue, green, red, far-red, white) added to white background light for seven days. Changes in the global metabolome of the fruit pericarp were monitored using LCMS and GCMS (554 compounds in total). Health-beneficial compounds (carotenoids, flavonoids, tocopherols and phenolic acids) accumulated faster under white light compared to darkness, while alkaloids and chlorophylls decreased faster. Light also changed the levels of taste-related metabolites including glutamate and malate. The light spectrum treatments indicated that the addition of blue light was the most effective treatment in altering the fruit metabolome. We conclude that light during ripening of tomatoes can have various effects on the metabolome and may help with shaping the levels of key compounds involved in various fruit quality characteristics.
    Mimicry of emergent traits amplifies coastal restoration success
    Temmink, Ralph J.M. ; Christianen, Marjolijn J.A. ; Fivash, Gregory S. ; Angelini, Christine ; Boström, Christoffer ; Didderen, Karin ; Engel, Sabine M. ; Esteban, Nicole ; Gaeckle, Jeffrey L. ; Gagnon, Karine ; Govers, Laura L. ; Infantes, Eduardo ; Katwijk, Marieke M. van; Kipson, Silvija ; Lamers, Leon P.M. ; Lengkeek, Wouter ; Silliman, Brian R. ; Tussenbroek, Brigitta I. van; Unsworth, Richard K.F. ; Yaakub, Siti Maryam ; Bouma, Tjeerd J. ; Heide, Tjisse van der - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Restoration is becoming a vital tool to counteract coastal ecosystem degradation. Modifying transplant designs of habitat-forming organisms from dispersed to clumped can amplify coastal restoration yields as it generates self-facilitation from emergent traits, i.e. traits not expressed by individuals or small clones, but that emerge in clumped individuals or large clones. Here, we advance restoration science by mimicking key emergent traits that locally suppress physical stress using biodegradable establishment structures. Experiments across (sub)tropical and temperate seagrass and salt marsh systems demonstrate greatly enhanced yields when individuals are transplanted within structures mimicking emergent traits that suppress waves or sediment mobility. Specifically, belowground mimics of dense root mats most facilitate seagrasses via sediment stabilization, while mimics of aboveground plant structures most facilitate marsh grasses by reducing stem movement. Mimicking key emergent traits may allow upscaling of restoration in many ecosystems that depend on self-facilitation for persistence, by constraining biological material requirements and implementation costs.

    Pontiella desulfatans gen. Nov., sp. nov., and pontiella sulfatireligans sp. nov., two marine anaerobes of the pontiellaceae fam. nov. producing sulfated glycosaminoglycan-like exopolymers
    Vliet, Daan M. van; Lin, Yuemei ; Bale, Nicole J. ; Koenen, Michel ; Villanueva, Laura ; Stams, Alfons J.M. ; Sánchez-Andrea, Irene - \ 2020
    Microorganisms 8 (2020)6. - ISSN 2076-2607 - p. 1 - 22.
    Black Sea - CAZymes - Glycosaminoglycans - Kiritimatiella - Novel anaerobes

    Recently, we isolated two marine strains, F1T and F21T, which together with Kiritimatiella glycovorans L21-Fru-ABT are the only pure cultures of the class Kiritimatiellae within the phylum Verrucomicrobiota. Here, we present an in-depth genome-guided characterization of both isolates with emphasis on their exopolysaccharide synthesis. The strains only grew fermentatively on simple carbohydrates and sulfated polysaccharides. Strains F1T, F21T and K. glycovorans reduced elemental sulfur, ferric citrate and anthraquinone-2,6-disulfonate during anaerobic growth on sugars. Both strains produced exopolysaccharides during stationary phase, probably with intracellularly stored glycogen as energy and carbon source. Exopolysaccharides included N-sulfated polysaccharides probably containing hexosamines and thus resembling glycosaminoglycans. This implies that the isolates can both degrade and produce sulfated polysaccharides. Both strains encoded an unprecedently high number of glycoside hydrolase genes (422 and 388, respectively), including prevalent alpha-L-fucosidase genes, which may be necessary for degrading complex sulfated polysaccharides such as fucoidan. Strain F21T encoded three putative glycosaminoglycan sulfotransferases and a putative sulfate glycosaminoglycan biosynthesis gene cluster. Based on phylogenetic and chemotaxonomic analyses, we propose the taxa Pontiella desulfatans F1T gen. nov., sp. nov. and Pontiella sulfatireligans F21T sp. nov. as representatives of the Pontiellaceae fam. nov. within the class Kiritimatiellae.

    Phenotypic and lifestyle determinants of HbA1c in the general population – the Hoorn study
    Wisgerhof, Willem ; Ruijgrok, Carolien ; Braver, Nicole R. Den; Borgonjen—van Den Berg, Karin J. ; Heijden, Amber A.W.A. Van Der; Elders, Petra J.M. ; Beulens, Joline W.J. ; Alssema, Marjan - \ 2020
    PLoS ONE 15 (2020)6. - ISSN 1932-6203

    Aim To investigate the relative contribution of phenotypic and lifestyle factors to HbA1c, independent of fasting plasma glucose (FPG) and 2h post-load glucose (2hPG), in the general population. Methods The study populations included 2309 participants without known diabetes from the first wave of the Hoorn Study (1989) and 2619 from the second wave (2006). Multivariate linear regression models were used to analyze the relationship between potential determinants and HbA1c in addition to FPG and 2hPG. The multivariate model was derived in the first wave of the Hoorn Study, and replicated in the second wave. Results In both cohorts, independent of FPG and 2hPG, higher age, female sex, larger waist circumference, and smoking were associated with a higher HbA1c level. Larger hip circumference, higher BMI, higher alcohol consumption and vitamin C intake were associated with a lower HbA1c level. FPG and 2hPG together explained 41.0% (first wave) and 53.0% (second wave) of the total variance in HbA1c. The combination of phenotypic and lifestyle determinants additionally explained 5.7% (first wave) and 3.9% (second wave). Conclusions This study suggests that, independent of glucose, phenotypic and lifestyle factors are associated with HbA1c, but the contribution is relatively small. These findings contribute to a better understanding of the low correlation between glucose levels and HbA1c in the general population.

    Lighting the way for increased vitamin C in tomatoes
    Ntagkas, Nikolaos - \ 2020
    Wageningen University. Promotor(en): L.F.M. Marcelis; E.J. Woltering, co-promotor(en): C.C.S Nicole. - Wageningen : Wageningen University - ISBN 9789463954013 - 153
    Are dual-purpose hens less fearful than conventional layer hybrids?
    Giersberg, Mona Franziska ; Spindler, Birgit ; Kemper, Nicole - \ 2020
    Veterinary Record (2020). - ISSN 0042-4900
    behaviour - husbandry - laying hens - welfare

    Background: Excessive fear in farm animals can lead to chronic stress and thus impair animal welfare. In laying hens, fear responses in several behavioural tests have also been associated with the occurrence of feather pecking. The aim of the present study was to comparatively assess fear-related responses of conventional layer hybrids (Lohmann Brown plus, LB+) and dual-purpose hens (Lohmann Dual, LD), which seem to be less prone to injurious pecking. Methods: A novel object (NO) and an avoidance distance (AD) test were carried out in both hybrids at a group level and at different ages during the laying period in order to measure their fear-related responses. Results: On most study days, more LD hens approached the NO and they approached it sooner than the LB+ hens. Similarly, the LD hens retreated at smaller distances from a human being in the AD test. Conclusion: The results indicate that dual-purpose hens act less fearful in the performed behavioural tests compared with conventional layer hybrids. Therefore, dual-purpose hens might experience less stress during daily management routines, which would affect animal welfare positively.

    Visualizing the invisible : class excursions to ignite children’s enthusiasm for microbes
    McGenity, Terry J. ; Gessesse, Amare ; Hallsworth, John E. ; Garcia Cela, Esther ; Verheecke-Vaessen, Carol ; Wang, Fengping ; Chavarría, Max ; Haggblom, Max M. ; Molin, Søren ; Danchin, Antoine ; Smid, Eddy J. ; Lood, Cédric ; Cockell, Charles S. ; Whitby, Corinne ; Liu, Shuang Jiang ; Keller, Nancy P. ; Stein, Lisa Y. ; Bordenstein, Seth R. ; Lal, Rup ; Nunes, Olga C. ; Gram, Lone ; Singh, Brajesh K. ; Webster, Nicole S. ; Morris, Cindy ; Sivinski, Sharon ; Bindschedler, Saskia ; Junier, Pilar ; Antunes, André ; Baxter, Bonnie K. ; Scavone, Paola ; Timmis, Kenneth - \ 2020
    Microbial Biotechnology (2020). - ISSN 1751-7907

    We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology-literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513-1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public-health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well-being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination-capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision-making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology-centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre-occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.

    Reproducible molecular networking of untargeted mass spectrometry data using GNPS
    Aron, Allegra T. ; Gentry, Emily C. ; McPhail, Kerry L. ; Nothias, Louis Félix ; Nothias-Esposito, Mélissa ; Bouslimani, Amina ; Petras, Daniel ; Gauglitz, Julia M. ; Sikora, Nicole ; Vargas, Fernando ; Hooft, Justin J.J. van der; Ernst, Madeleine ; Kang, Kyo Bin ; Aceves, Christine M. ; Caraballo-Rodríguez, Andrés Mauricio ; Koester, Irina ; Weldon, Kelly C. ; Bertrand, Samuel ; Roullier, Catherine ; Sun, Kunyang ; Tehan, Richard M. ; Boya P, Cristopher A. ; Christian, Martin H. ; Gutiérrez, Marcelino ; Ulloa, Aldo Moreno ; Tejeda Mora, Javier Andres ; Mojica-Flores, Randy ; Lakey-Beitia, Johant ; Vásquez-Chaves, Victor ; Zhang, Yilue ; Calderón, Angela I. ; Tayler, Nicole ; Keyzers, Robert A. ; Tugizimana, Fidele ; Ndlovu, Nombuso ; Aksenov, Alexander A. ; Jarmusch, Alan K. ; Schmid, Robin ; Truman, Andrew W. ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
    Nature protocols 15 (2020). - ISSN 1754-2189 - p. 1954 - 1991.

    Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking—one of the main analysis tools used within the GNPS platform—creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

    Marine mammal surveys in Dutch North Sea waters in 2019
    Geelhoed, Steve C.V. ; Janinhoff, Nicole ; Lagerveld, Sander ; Verdaat, Hans - \ 2020
    Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C016/20) - 22
    Aerial surveys to estimate the abundance of Harbour Porpoise Phocoena phocoena were conducted on the Dutch Continental Shelf in summer 2019. These surveys followed predetermined track lines in four areas: A - Dogger Bank, B - Offshore, C - Frisian Front & D - Delta. Between 16 July and 4 August the entire Dutch Continental Shelf (DCS) was surveyed. Marine mammals were assessed using line transect distance sampling methods. Density and abundance estimates were calculated. In total, 150 sightings of 189 individual Harbour Porpoises were collected. Porpoise densities varied between 0.54-1.76 animals/km² in the areas A-D. The overall density was 0.66 animals/km². The lowest density (0.46 animals/km²) was recorded in area A – Dogger Bank. The densities in the other areas were in the same order of magnitude, ranging between 0.68-071 animals/km². In summer 2019 the total number of Harbour Porpoises on the Dutch Continental Shelf (areas A-D) was estimated at 38,911 individuals (CI = 20,791-76,822). This estimates falls in the range of abundance estimates since 2010, with a minimum of 25,998 (CI = 13,988 – 53,623 in 2010) and a maximum of 76,773 (CI = 43,414-154,265 in 2014) individuals. The confidence intervals of the abundance estimates overlap, indicating no statistically significant differences between the years. The time series, however, is relatively short to measure trends. These abundance estimates show that up to a fifth of the North Sea population, estimated at 345,000-361,000 individuals, has been present on the Dutch Continental Shelf during the summer surveys in 2010-2019. The results of these aerial surveys will feed into the OSPAR MSFD indicator on abundance and distribution of marine mammals. In total 26 sightings of other marine mammal species than Harbour Porpoises were recorded. These comprised 22 sightings of seals (Grey Seal Halichoerus grypus and Harbour Seal Phoca vitulina). The majority of the seals was observed in coastal waters off the Wadden Isles. Three single Minke Whales Balaenoptera acutorostrata were seen (feeding) in area A – Dogger Bank and B – Offshore, with another one sighted off effort in the same area. One sighting of a pod of two White-beaked Dolphins Lagenorhynchus albirostris was made in area B – Offshore. This research is part of the BO-project ‘monitoring bruinvis’.
    Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication
    Hulme, Heather ; Meikle, Lynsey M. ; Strittmatter, Nicole ; Hooft, Justin J.J. van der; Swales, John ; Bragg, Ryan A. ; Villar, Victor H. ; Ormsby, Michael J. ; Barnes, Stephanie ; Brown, Sheila L. ; Dexter, Alex ; Kamat, Maya T. ; Komen, Jasper C. ; Walker, Daniel ; Milling, Simon ; Osterweil, Emily K. ; MacDonald, Andrew S. ; Schofield, Chris J. ; Tardito, Saverio ; Bunch, Josephine ; Douce, Gillian ; Edgar, Julia M. ; Edrada-Ebel, Ru Angelie ; Goodwin, Richard J.A. ; Burchmore, Richard ; Wall, Daniel M. - \ 2020
    Science Advances 6 (2020)11. - ISSN 2375-2548

    Alterations to the gut microbiome are associated with various neurological diseases, yet evidence of causality and identity of microbiome-derived compounds that mediate gut-brain axis interaction remain elusive. Here, we identify two previously unknown bacterial metabolites 3-methyl-4-(trimethylammonio)butanoate and 4-(trimethylammonio)pentanoate, structural analogs of carnitine that are present in both gut and brain of specific pathogen-free mice but absent in germ-free mice. We demonstrate that these compounds are produced by anaerobic commensal bacteria from the family Lachnospiraceae (Clostridiales) family, colocalize with carnitine in brain white matter, and inhibit carnitine-mediated fatty acid oxidation in a murine cell culture model of central nervous system white matter. This is the first description of direct molecular inter-kingdom exchange between gut prokaryotes and mammalian brain cells, leading to inhibition of brain cell function.

    Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    Following publication of this Data Descriptor it was found that the affiliation of Oliver Purschke was stated incorrectly. The correct affiliations are stated below: Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden Biodiversity, Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden This has been corrected in both the HTML and PDF versions.

    Evolution of vascular plants through redeployment of ancient developmental regulators
    Lu, Kuan Ju ; van’t Wout Hofland, Nicole ; Mor, Eliana ; Mutte, Sumanth ; Abrahams, Paul ; Kato, Hirotaka ; Vandepoele, Klaas ; Weijers, Dolf ; Rybel, Bert de - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)1. - ISSN 0027-8424 - p. 733 - 740.
    Heterodimerization - Plant evolution - Plant vascular tissues - TMO5/LHW - Tracheophytes

    Vascular plants provide most of the biomass, food, and feed on earth, yet the molecular innovations that led to the evolution of their conductive tissues are unknown. Here, we reveal the evolutionary trajectory for the heterodimeric TMO5/LHW transcription factor complex, which is rate-limiting for vascular cell proliferation in Arabidopsis thaliana. Both regulators have origins predating vascular tissue emergence, and even terrestrialization. We further show that TMO5 evolved its modern function, including dimerization with LHW, at the origin of land plants. A second innovation in LHW, coinciding with vascular plant emergence, conditioned obligate heterodimerization and generated the critical function in vascular development in Arabidopsis. In summary, our results suggest that the division potential of vascular cells may have been an important factor contributing to the evolution of vascular plants.

    Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
    Strepis, Nikolaos ; Naranjo, Henry D. ; Meier-Kolthoff, Jan ; Göker, Markus ; Shapiro, Nicole ; Kyrpides, Nikos ; Klenk, Hans Peter ; Schaap, Peter J. ; Stams, Alfons J.M. ; Sousa, Diana Z. - \ 2020
    BMC Genomics 21 (2020)1. - ISSN 1471-2164
    1,3-propanediol - Comparative genomics - Halophilic - Protein domains - Psychrophilic

    Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

    A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

    Towards harmonization of test methods for in vitro hepatic clearance studies
    Louisse, Jochem ; Alewijn, Martin ; Peijnenburg, Ad A.C.M. ; Cnubben, Nicole H.P. ; Heringa, Minne B. ; Coecke, Sandra ; Punt, Ans - \ 2020
    Toxicology in Vitro 63 (2020). - ISSN 0887-2333 - 1 p.

    Non-animal methods for toxicokinetics, such as in vitro hepatic metabolic clearance studies, play an important role in chemical risk evaluations. To gain regulatory acceptance of such clearance data, the development of a test guideline for performing in vitro hepatic clearance studies is crucial. The aim of the present study was to obtain insight in the experimental conditions of clearance studies that influence obtained intrinsic clearance (CLint) values. To that end, in vitro hepatic CLint data obtained with rat or human hepatocytes and methodological aspects of the experiments, were collected from 42 different suitable studies published between 1995 and 2018. The CLint values for the majority of chemicals differed by more than one order of magnitude. We estimated the systematic effect of different experimental setups on the CLint values using a random forest regression analysis, revealing that 'hepatocyte concentration', 'species' (rat or human hepatocytes) and 'culture medium' have the largest impact. Calculating unbound CLint (CLint,u) values slightly reduced the variation for most chemicals. Given that in vivo clearance is in general underpredicted based on in vitro clearance data, a harmonized protocol is preferably based on a protocol that provides relatively high in vitro CLint values.

    Mass spectrometry searches using MASST
    Wang, Mingxun ; Jarmusch, Alan K. ; Vargas, Fernando ; Aksenov, Alexander A. ; Gauglitz, Julia M. ; Weldon, Kelly ; Petras, Daniel ; Silva, Ricardo da; Quinn, Robert ; Melnik, Alexey V. ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Aceves, Christine M. ; Panitchpakdi, Morgan ; Brown, Elizabeth ; Ottavio, Francesca Di; Sikora, Nicole ; Elijah, Emmanuel O. ; Labarta-Bajo, Lara ; Gentry, Emily C. ; Shalapour, Shabnam ; Kyle, Kathleen E. ; Puckett, Sara P. ; Watrous, Jeramie D. ; Carpenter, Carolina S. ; Bouslimani, Amina ; Ernst, Madeleine ; Swafford, Austin D. ; Zúñiga, Elina I. ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Loomba, Rohit ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Nature Biotechnology 38 (2020). - ISSN 1087-0156 - p. 23 - 26.
    Portioning meat and vegetables in four different out of home settings : A win-win for guests, chefs and the planet
    Reinders, Machiel J. ; Lieshout, Lilou van; Pot, Gerda K. ; Neufingerl, Nicole ; Broek, Eva van den; Battjes-Fries, Marieke ; Heijnen, Joris - \ 2020
    Appetite 147 (2020). - ISSN 0195-6663
    Environmental impact - Healthy diet - Meat - Plant-forward diet - Portion size - Real-life intervention study - Restaurant - Vegetables

    Individuals increasingly consume their meals away from home. This article describes a series of studies that examined the effects of meals with reduced amounts of meat and increased amounts of vegetables on food consumption, waste and guest satisfaction in four real-life restaurant settings in the Netherlands: an a-la-carte restaurant, six company canteens, a self-service restaurant, and a buffet restaurant, including nearly 1500 participants in total. The four studies in these four different out of home settings consistently showed that adapting portion sizes of meat and vegetables was effective to reduce meat consumption and increase vegetable consumption, while maintaining high guest satisfaction. Guest satisfaction even increased when vegetables were presented and prepared in a more attractive and tasty way. Thus, adapting portion sizes of meat and vegetables provides a viable strategy to stimulate healthy and environmentally sustainable consumption patterns in out of home settings.

    The politics of co-production: participation, power, and transformation
    Turnhout, E. ; Metze, T.A.P. ; Wyborn, Carina ; Klenk, Nicole ; Louder, Elena - \ 2020
    Current Opinion in Environmental Sustainability 42 (2020). - ISSN 1877-3435 - p. 15 - 21.
    Literature on co-production is booming. Yet, most literature is aspirational and methodological in nature, focusing on why co-production is important for environmental governance and knowledge production and how it should be done, and does not address the question why these processes often fail to achieve stated objectives of empowerment and societal transformation. In this review, we address this gap by reviewing literature on the political and power dimensions of co-production. Our review shows how depoliticization dynamics in co-production reinforce rather than mitigate existing unequal power relations and how they prevent wider societal transformation from taking place. Drawing on literature about participation, deliberative governance, and democracy, the review concludes by emphasizing the importance of (re)politicizing co-production by allowing for pluralism and for the contestation of knowledge.
    Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
    Gauglitz, Julia M. ; Aceves, Christine M. ; Aksenov, Alexander A. ; Aleti, Gajender ; Almaliti, J. ; Bouslimani, A. ; Brown, Elizabeth A. ; Campeau, Anaamika ; Caraballo-Rodríguez, Andrés Mauricio ; Chaar, Rama ; Silva, Ricardo R. da; Demko, Alyssa M. ; Ottavio, Francesca Di; Elijah, Emmanuel ; Ernst, Madeleine ; Ferguson, L.P. ; Holmes, Xavier ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kang, Kyo Bin ; Koester, I. ; Kwan, B. ; Li, Jie ; Li, Yueying ; Melnik, Alexey V. ; Molina-Santiago, Carlos ; Ni, B. ; Oom, Aaron L. ; Panitchpakdi, Morgan W. ; Petras, Daniel ; Quinn, Robert ; Sikora, Nicole ; Spengler, Katharina ; Teke, B. ; Tripathi, Anupriya ; Ul-Hasan, S. ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vrbanac, Alison ; Vu, Anthony Q. ; Wang, Steven C. ; Weldon, K. ; Wilson, K. ; Wozniak, Jacob M. ; Yoon, Michael ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Food Chemistry 302 (2020). - ISSN 0308-8146
    Fermentation - Food - LC-MS/MS - Metabolomics - Molecular networking - Tea - Untargeted mass spectrometry - Yogurt

    In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.

    Usable environmental knowledge from the perspective of decision-making: the logics of consequentiality, appropriateness, and meaningfulness
    Dewulf, Art ; Klenk, Nicole ; Wyborn, Carina ; Lemos, Maria Carmen - \ 2020
    Current Opinion in Environmental Sustainability 42 (2020). - ISSN 1877-3435 - p. 1 - 6.

    Environmental knowledge is a crucial input for public and private decision-making, yet often useful environmental knowledge appears to be unusable for decision-makers. To better understand how usable knowledge can be produced, we need to build on a better understanding of decision-making processes. We distinguish three different logics of decision-making and discuss their implications for knowledge use: (1) the logic of consequentiality, rooted in theories of rational choice, in which environmental knowledge is used because of its utilitarian value; (2) the logic of appropriateness, rooted in institutional theories, in which environmental knowledge is used because it fits existing rules and routines; and (3) the logic of meaningfulness, rooted in theories of sensemaking and interpretation, in which environmental knowledge is used because it makes sense to decision-makers. The theory and practice of environmental knowledge (co-)production can profit from considering these different logics of decision-making.

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