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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Bridging ICTs with governance capabilities for food–energy–water sustainability : Emergent Governance Studies
Karpouzoglou, T.D. ; Pereira, L. ; Doshi, S. - \ 2018
In: Food, Energy and Water Sustainability: Eemergent Governance Strategies / Pereira, Laura M., McElroy, Caitlin, Littaye, Alexandra, Girard, Alexandra M., Routledge, Taylor & Francis Group (Earthscan Studies in Natural Resource Management ) - ISBN 9781315696522 - p. 222 - 238.
In this chapter, we critically explore the important role that Information and Communication Technologies (ICTs) play in food, energy, and water (FEW) governance. In particular, we perceive an important role for ICTs in bridging the knowledge gap associated with FEW development goals and for addressing the many synergies and trade-offs between these goals and existing governance arrangements (Mol, 2006; UN, 2014; WWAP, 2015). FEW governance presents us with a ‘wicked’ problem in that it is unstructured, complex, and contains multiple and interconnected subsets of problems (Weber & Khademanian, 2009). A wicked problem can be understood as a problem that is typically ill-defined and involves many uncertainties and contrary views of how to address it (Dewulf & Termeer, 2015). In a similar way in which climate change adaptation is a wicked problem, FEW governance cannot be precisely formulated or solved due to diverging understandings of FEW development priorities as well as inherent complexities associated with their monitoring and evaluation (Murthy et al., 2013). Yet, FEW governance is becoming a key political priority as the adoption of the Sustainable Development Goals (SDGs) places huge importance on FEW systems and the need for putting in place a comprehensive monitoring framework to track progress towards global sustainability (EAT Initiative, 2015). It is in this context that we envisage ICTs will play a substantial role in creating better conditions for FEW governance and thus aid in achieving the SDGs over the coming years.
Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake
Middleton, Alistair M. ; Bosco, Cristina Dal; Chlap, Phillip ; Bensch, Robert ; Harz, Hartmann ; Ren, Fugang ; Bergmann, Stefan ; Wend, Sabrina ; Weber, Wilfried ; Hayashi, Ken Ichiro ; Zurbriggen, Matias D. ; Uhl, Rainer ; Ronneberger, Olaf ; Palme, Klaus ; Fleck, Christian ; Dovzhenko, Alexander - \ 2018
Cell Reports 22 (2018)11. - ISSN 2211-1247 - p. 3044 - 3057.
auxin - auxin flux - auxin sensor - endoplasmic reticulum - fluorescent aux - mathematical modeling - microscopy - nucleus - protoplasts - single cells
In plants, the phytohormone auxin acts as a master regulator of developmental processes and environmental responses. The best characterized process in the auxin regulatory network occurs at the subcellular scale, wherein auxin mediates signal transduction into transcriptional programs by triggering the degradation of Aux/IAA transcriptional repressor proteins in the nucleus. However, whether and how auxin movement between the nucleus and the surrounding compartments is regulated remain elusive. Using a fluorescent auxin analog, we show that its diffusion into the nucleus is restricted. By combining mathematical modeling with time course assays on auxin-mediated nuclear signaling and quantitative phenotyping in single plant cell systems, we show that ER-to-nucleus auxin flux represents a major subcellular pathway to directly control nuclear auxin levels. Our findings propose that the homeostatically regulated auxin pool in the ER and ER-to-nucleus auxin fluxes underpin auxin-mediated downstream responses in plant cells. Middleton et al. study how the plant phytohormone auxin enters the nucleus by using quantitative phenotyping in single plant cell systems and bespoke mathematical models that relate controlled perturbations to experimentally measurable responses. Their findings show that auxin predominantly enters the nucleus via the endoplasmic reticulum.
Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection
Barkema, H.W. ; Orsel, K. ; Nielsen, S. ; Koets, Ad ; Rutten, V.P.M.G. ; Bannantine, J.P. ; Keefe, G.P. ; Kelton, D.F. ; Wells, S.J. ; Whittington, R.J. ; Mackintosh, C.G. ; Manning, E.J. ; Weber, M.F. ; Heuer, C. ; Forde, T.L. ; Ritter, C. ; Roche, S. ; Corbett, C.S. ; Wolf, R. ; Griebel, P.J. ; Kastelic, J.P. ; Buck, J. De - \ 2018
Transboundary and Emerging Diseases 65 (2018)S1. - ISSN 1865-1674 - p. 125 - 148.
In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps
3C in maize and arabidopsis
Weber, Blaise ; Jamge, Suraj ; Stam, Maike - \ 2018
In: Methods in Molecular Biology Humana Press Inc. (Methods in Molecular Biology ) - p. 247 - 270.
3C protocol - Arabidopsis thaliana - Chromosome Conformation Capture - Plant - Zea mays
With Chromosome Conformation Capture (3C), the relative interaction frequency of one chromosomal fragment with another can be determined. The technique is especially suited for unraveling the 3D organization of specific loci when focusing on aspects such as enhancer–promoter interactions or other topological conformations of the genome. 3C has been extensively used in animal systems, among others providing insight into gene regulation by distant cis-regulatory elements. In recent years, the 3C technique has been applied in plant research. However, the complexity of plant tissues prevents direct application of existing protocols from animals. Here, we describe an adapted protocol suitable for plant tissues, especially Arabidopsis thaliana and Zea mays.
Paratuberculose in (melk)geiten : Nieuwe inzichten en praktische handvatten
Lievaart-Peterson, K. ; Bokma-Bakker, M.H. ; Luttikholt, S. ; Koets, A.P. ; Weber, M. ; Vellema, P. ; Antonis, A.F.G. - \ 2017
Wageningen : Wageningen University & Research - 8 p.
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
Blin, Kai ; Kim, Hyun Uk ; Medema, M.H. ; Weber, Tilmann - \ 2017
Briefings in Bioinformatics (2017). - ISSN 1467-5463 - 11 p.
Many drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic gene clusters (BGCs) and follow a highly conserved biosynthetic logic. This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. However, mining for a variety of BGCs quickly approaches a complexity level where manual analyses are no longer possible and require the use of automated genome mining pipelines, such as the antiSMASH software. In this review, we discuss the principles underlying the predictions of antiSMASH and other tools and provide practical advice for their application. Furthermore, we discuss important caveats such as rule-based BGC detection, sequence and annotation quality and cluster boundary prediction, which all have to be considered while planning for, performing and analyzing the results of genome mining studies.
Retamoid scrubs of the Cytisetea scopario-striati in the Netherlands : A new approach to classify marginal associations
Haveman, R. ; Ronde, I. de; Schaminée, Joop H.J. - \ 2017
Tuexenia 37 (2017). - ISSN 0722-494X - p. 143 - 161.
Character species - Chorological tension zone - Classification - Cytisus scoparius - Differential species - Distribution area - Synchorology - Syntaxonomy - Ulex europaeus

Marginal associations, i.e. floristically impoverished associations at the margin of the distribution area of a higher syntaxon, form a problem in vegetation classification, because true character species are lacking. We propose a new approach for the classification of such marginal associations, making use of the notion of 'chorological tension zones'. In the absence of true character species, the species from other syntaxa of the same formation can be used as such. Our proposal is to use the species group from every formation-true class only once within every marginal alliance, to limit the number of possible marginal associations. This approach is illustrated in a classification of the retamoid thickets in the Netherlands. On the basis of a numerical-subjective classification of the relevant species in the scrub layer and the evaluation of relevant literature, we conclude that the broom and gorse thickets in the Netherlands can be assigned to the Cytisetea scopario-striati Rivas-Mart. 1974, which is represented by four associations, each of which is characterised by the species of other scrub classes. The Ulici europaei- Sarothamnion scoparii Doing ex Weber 1997 is represented by the Rubo plicati-Sarothamnetum scoparii Weber 1987 and the Crataego monogynae-Cytisetum scoparii R. Haveman, I. de Ronde & J.H.J. Schaminée ass. nov., the Ulici europaei-Cytision striati Rivas-Mart., Báscones, Díaz, Fern. Gonz. & Loidi 1991 by the Frangulo alni-Ulicetum europaei De Foucault 1988 and the Rubo ulmifolii- Ulicetum europaei J.-M. Géhu ex R. Haveman, I. de Ronde & J.H.J. Schaminée ass. nov. This classification is based on a restricted dataset though, and a revision, based on a larger dataset from a wider region has to prove the tenability of the classification.

Institutionalizing environmental reform with sense-making: West and Central Africa ports and the ‘green port’ phenomenon
Barnes Dabban, H. ; Tatenhove, J.P.M. van; Koppen, C.S.A. van; Termeer, C.J.A.M. - \ 2017
Marine Policy 86 (2017). - ISSN 0308-597X - p. 111 - 120.
Harmonizing economic activities with environmental considerations has emerged as a new globalizing phenomenon for ports. The phenomenon is labelled as ‘green port’. There is however no canonical way of turning green port into business reality. Some advanced ports have adapted it and African ports are also beginning to follow. The Freeport of Monrovia in West and Central Africa had its process of incorporating environmental considerations into its operational practices in an environmental reform labelled as ‘going green’, akin to the green port phenomenon. The process interrupted routinized port activities and behavior. Employees of Freeport of Monrovia and stakeholders could not foresee the meaning and consequences of such reform. The uncertainty triggered a process for employees and stakeholders to collectively make sense of and react to their new situation. This paper integrates Weick's sense-making properties with Weber and Glynn's institutional mechanisms affiliated to sense-making as a conceptual tool to analyze and understand the process by which meaning was assigned to Freeport of Monrovia's environmental reform and also how it became institutionalized. The analysis is based on hands-on empirical research on an environmental capacity strengthening project executed in 2013 in the Freeport of Monrovia as part of its institutional reform from a service port into landlord port. Findings bring to light the dynamic interplay of institutions and sense-making in the greening of Freeport of Monrovia.
Ontwikkeling WMR Benthos Separator : Testen en ontwikkelen van een stroomgoot voor het scheiden van macrozoöbenthos van grof sediment
Coolen, J.W.P. ; Weber, C.L. ; Weide, B.E. van der; Jak, R.G. - \ 2017
IJmuiden : Wageningen Marine Research (Wageningen Marine Research rapport C073/17) - 27
Public health relevance of drug–nutrition interactions
Péter, Szabolcs ; Navis, Gerjan ; Borst, Martin H. de; Schacky, Clemens von; Orten-Luiten, Anne Claire B. van; Zhernakova, Alexandra ; Witkamp, Renger F. ; Janse, André ; Weber, Peter ; Bakker, Stephan L.J. ; Eggersdorfer, Manfred - \ 2017
European Journal of Nutrition 56 (2017)suppl. 2. - ISSN 1436-6207 - p. 23 - 36.
Drug–nutrient interactions - Health benefits - Microbiota - Micronutrient deficiency - Public health
The public health relevance of drug–nutrition interactions is currently highly undervalued and overlooked. This is particularly the case for elderly persons where multi-morbidity and consequently polypharmacy is very common. Vitamins and other micronutrients have central functions in metabolism, and their interactions with drugs may result in clinically relevant physiological impairments but possibly also in positive effects. On 12 April 2016, the University Medical Center Groningen (The Netherlands), as part of its Healthy Ageing program, organized a workshop on the public health relevance of drug–nutrient interactions. In this meeting, experts in the field presented results from recent studies on interactions between pharmaceuticals and nutrients, and discussed the role of nutrition for elderly, focusing on those persons receiving pharmaceutical treatment. This paper summarizes the proceedings of the symposium and provides an outlook for future research needs and public health measures. Since food, pharma and health are closely interconnected domains, awareness is needed in the medical community about the potential relevance of drug–nutrition interactions. Experts and stakeholders should advocate for the integration of drug–nutrition evaluations in the drug development process. Strategies for the individual patients should be developed, by installing drug review protocols, screening for malnutrition and integrating this topic into the general medical advice.
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification
Blin, Kai ; Wolf, Thomas ; Chevrette, Marc G. ; Lu, Xiaowen ; Schwalen, Christopher J. ; Kautsar, Satria A. ; Suarez Duran, Hernando G. ; Los Santos, Emmanuel L.C. De; Kim, Hyun Uk ; Nave, Mariana ; Dickschat, Jeroen S. ; Mitchell, Douglas A. ; Shelest, Ekaterina ; Breitling, Rainer ; Takano, Eriko ; Lee, Sang Yup ; Weber, Tilmann ; Medema, Marnix H. - \ 2017
Nucleic Acids Research 45 (2017)W1. - ISSN 0305-1048 - p. W36 - W41.
Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
Naturalized alien flora of the world : Species diversity, taxonomic and phylogenetic patterns, geographic distribution and global hotspots of plant invasion
Pyšek, Petr ; Pergl, Jan ; Essl, Franz ; Lenzner, Bernd ; Dawson, Wayne ; Kreft, Holger ; Weigelt, Patrick ; Winter, Marten ; Kartesz, John ; Nishino, Misako ; Antonova, Liubov A. ; Barcelona, Julie F. ; Cabezas, Francisco J. ; Cárdenas, Dairon ; Cárdenas-Toro, Juliana ; Castaño, Nicolás ; Chacón, Eduardo ; Chatelain, Cyrille ; Dullinger, Stefan ; Ebel, Aleksandr L. ; Figueiredo, Estrela ; Fuentes, Nicol ; Genovesi, Piero ; Groom, Quentin J. ; Henderson, Lesley ; Inderjit, ; Kupriyanov, Andrey ; Masciadri, Silvana ; Maurel, Noëlie ; Meerman, Jan ; Morozova, Olga ; Moser, Dietmar ; Nickrent, Daniel L. ; Nowak, Pauline M. ; Pagad, Shyama ; Patzelt, Annette ; Pelser, Pieter B. ; Seebens, Hanno ; Shu, Wen Sheng ; Thomas, Jacob ; Velayos, Mauricio ; Weber, Ewald ; Wieringa, Jan J. ; Baptiste, María P. ; Kleunen, Mark Van - \ 2017
Preslia 89 (2017)3. - ISSN 0032-7786 - p. 203 - 274.
Alien species - Distribution - Global Naturalized Alien Flora (GloNAF) database - Invasive species - Islands - Life history - Mainland - Naturalized species - Phylogeny - Plant invasion - Regional floras - Species richness - Taxonomy - Zonobiome
Using the recently built Global Naturalized Alien Flora (GloNAF) database, containing data on the distribution of naturalized alien plants in 483 mainland and 361 island regions of the world, we describe patterns in diversity and geographic distribution of naturalized and invasive plant species, taxonomic, phylogenetic and life-history structure of the global naturalized flora as well as levels of naturalization and their determinants. The mainland regions with the highest numbers of naturalized aliens are some Australian states (with New South Wales being the richest on this continent) and several North American regions (of which California with 1753 naturalized plant species represents the world's richest region in terms of naturalized alien vascular plants). England, Japan, New Zealand and the Hawaiian archipelago harbour most naturalized plants among islands or island groups. These regions also form the main hotspots of the regional levels of naturalization, measured as the percentage of naturalized aliens in the total flora of the region. Such hotspots of relative naturalized species richness appear on both the western and eastern coasts of North America, in north-western Europe, South Africa, south-eastern Australia, New Zealand, and India. High levels of island invasions by naturalized plants are concentrated in the Pacific, but also occur on individual islands across all oceans. The numbers of naturalized species are closely correlated with those of native species, with a stronger correlation and steeper increase for islands than mainland regions, indicating a greater vulnerability of islands to invasion by species that become successfully naturalized. South Africa, India, California, Cuba, Florida, Queensland and Japan have the highest numbers of invasive species. Regions in temperate and tropical zonobiomes harbour in total 9036 and 6774 naturalized species, respectively, followed by 3280 species naturalized in the Mediterranean zonobiome, 3057 in the subtropical zonobiome and 321 in the Arctic. The New World is richer in naturalized alien plants, with 9905 species compared to 7923 recorded in the Old World. While isolation is the key factor driving the level of naturalization on islands, zonobiomes differing in climatic regimes, and socioeconomy represented by per capita GDP, are central for mainland regions. The 11 most widely distributed species each occur in regions covering about one third of the globe or more in terms of the number of regions where they are naturalized and at least 35% of the Earth's land surface in terms of those regions' areas, with the most widely distributed species Sonchus oleraceus occuring in 48% of the regions that cover 42% of the world area. Other widely distributed species are Ricinus communis, Oxalis corniculata, Portulaca oleracea, Eleusine indica, Chenopodium album, Capsella bursa-pastoris, Stellaria media, Bidens pilosa, Datura stramonium and Echinochloa crus-galli. Using the occurrence as invasive rather than only naturalized yields a different ranking, with Lantana camara (120 regions out of 349 for which data on invasive status are known), Calotropis procera (118), Eichhornia crassipes (113), Sonchus oleraceus (108) and Leucaena leucocephala (103) on top. As to the life-history spectra, islands harbour more naturalized woody species (34.4%) thanmainland regions (29.5%), and fewer annual herbs (18.7% compared to 22.3%). Ranking families by their absolute numbers of naturalized species reveals that Compositae (1343 species), Poaceae (1267) and Leguminosae (1189) contribute most to the global naturalized alien flora. Some families are disproportionally represented by naturalized aliens on islands (Arecaceae, Araceae, Acanthaceae, Amaryllidaceae, Asparagaceae, Convolvulaceae, Rubiaceae, Malvaceae), and much fewer so on mainland (e.g. Brassicaceae, Caryophyllaceae, Boraginaceae). Relating the numbers of naturalized species in a family to its total global richness shows that some of the large species-rich families are over-represented among naturalized aliens (e.g. Poaceae, Leguminosae, Rosaceae, Amaranthaceae, Pinaceae), some under-represented (e.g. Euphorbiaceae, Rubiaceae), whereas the one richest in naturalized species, Compositae, reaches a value expected from its global species richness. Significant phylogenetic signal indicates that families with an increased potential of their species to naturalize are not distributed randomly on the evolutionary tree. Solanum (112 species), Euphorbia (108) and Carex (106) are the genera richest in terms of naturalized species; over-represented on islands are Cotoneaster, Juncus, Eucalyptus, Salix, Hypericum, Geranium and Persicaria, while those relatively richer in naturalized species on the mainland are Atriplex, Opuntia, Oenothera, Artemisia, Vicia, Galium and Rosa. The data presented in this paper also point to where information is lacking and set priorities for future data collection. The GloNAF database has potential for designing concerted action to fill such data gaps, and provide a basis for allocating resources most efficiently towards better understanding and management of plant invasions worldwide.
Cyanodermella asteris sp. nov. (Ostropales) from the inflorescence axis of Aster tataricus
Jahn, Linda ; Schafhauser, Thomas ; Pan, Stefan ; Weber, Tilmann ; Wohlleben, Wolfgang ; Fewer, David P. ; Sivonen, Kaarina ; Flor, Liane ; Pée, Karl Heinz van; Caradec, Thibault ; Jacques, Philippe ; Huijbers, Mieke M.E. ; Berkel, Willem J.H. van; Ludwig-Müller, Jutta - \ 2017
Mycotaxon 132 (2017)1. - ISSN 0093-4666 - p. 107 - 123.
Ascomycota - Asteraceae - Lecanoromycetes - Pezizomycotina

An endophytic fungus isolated from the inflorescence axis of Aster tataricus is proposed as a new species. Phylogenetic analyses based on sequences from the ribosomal DNA cluster (the ITS1+5.8S+ITS2, 18S, and 28S regions) and the RPB2 gene revealed a relationship between the unknown fungus and the Stictidaceae lineage of the Ostropales. The new species, Cyanodermella asteris, grows in standard fungal growth media as a fluffy, pink filamentous fungus. Asexual and sexual sporulation has not yet been observed on media or in the plant.

Metabolic adaptation, a specialized leaf organ structure and vascular responses to diurnal N2 fixation by nostoc azollae sustain the astonishing productivity of azolla ferns without nitrogen fertilizer
Brouwer, Paul ; Bräutigam, Andrea ; Buijs, Valerie A. ; Tazelaar, Anne O.E. ; Werf, Adrie van der; Schlüter, Urte ; Reichart, Gert Jan ; Bolger, Anthony ; Usadel, Björn ; Weber, Andreas P.M. ; Schluepmann, Henriette - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Aquatic ferns - Azolla/nostoc azollae symbiosis - Clock evolution - Diel cycling - Dinitrogen fixation - Heterocystous cyanobacteria - Rna-seq - Vasculature
Sustainable agriculture demands reduced input of man-made nitrogen (N) fertilizer, yet N2 fixation limits the productivity of crops with heterotrophic diazotrophic bacterial symbionts. We investigated floating ferns from the genus Azolla that host phototrophic diazotrophic Nostoc azollae in leaf pockets and belong to the fastest growing plants. Experimental production reported here demonstrated N-fertilizer independent production of nitrogen-rich biomass with an annual yield potential per ha of 1200 kg-1 N fixed and 35 t dry biomass. 15N2 fixation peaked at noon, reaching 0.4 mg N g-1 dry weight h-1. Azolla ferns therefore merit consideration as protein crops in spite of the fact that little is known about the fern’s physiology to enable domestication. To gain an understanding of their nitrogen physiology, analyses of fern diel transcript profiles under differing nitrogen fertilizer regimes were combined with microscopic observations. Results established that the ferns adapted to the phototrophic N2-fixing symbionts N. azollae by (1) adjusting metabolically to nightly absence of N supply using responses ancestral to ferns and seed plants; (2) developing a specialized xylem-rich vasculature surrounding the leaf-pocket organ; (3) responding to N-supply by controlling transcripts of genes mediating nutrient transport, allocation and vasculature development. Unlike other non-seed plants, the Azolla fern clock is shown to contain both the morning and evening loops; the evening loop is known to control rhythmic gene expression in the vasculature of seed plants and therefore may have evolved along with the vasculature in the ancestor of ferns and seed plants.
Concealed diversity : taxonomical, phytogeographical and phytosociological notes on brambles (Rubus L. subgen. Rubus) in north-west Europe
Haveman, Rense - \ 2017
University. Promotor(en): Joop Schaminee, co-promotor(en): Rienk Jan Bijlsma. - Wageningen : Wageningen University - ISBN 9789463431019 - 200
rubus - diversity - taxonomy - phytogeography - geographical distribution - biogeography - apomixis - northwestern europe - diversiteit - taxonomie - plantengeografie - geografische verdeling - biogeografie - noordwest-europa

Rubus subgen. Rubus (bramble) is one of the large plant genera in Europe, consisting of only a few sexual biological species and at least 700 apomictic lineages. In this thesis, it is argued that the stabilised apomict lineages should best be regarded species, even if their distribution area doesn’t meet the requirements of a regional species as defined in several publications by Weber. Included is a checklist of Dutch bramble species, comprising 191 species belonging to Rubus subgen. Rubus. In the Netherlands, 97 of the 191 species are classified as regional species, with a distribution area diameter under 500 km. On the basis of distribution data of bramble species in Ireland, the UK, Denmark, Germany, and the Netherlands, 12 phytogeographical bramble-regions are distinguished. Although ecological factors play a role in the realisation of these regions, it is argued that the found patterns are primarily the result of evolutionary processes. The density and species composition of Rubus scrubs in the Netherlands is studied using landscape transects. At landscape scale, the bramble species in the scrubs are not randomly distributed, causing a spatial clustering of floristically similar bramble scrubs. It was concluded that only a part of the diversity of Rubus scrubs was accounted for in the Dutch national vegetation classification, and a new scrub type (the Rubetum taxandriae) was described on the basis of these findings. Rubus scrubs are an important biotope for rare shrub species and endemic Rubus species. Additionally, scrubs rich in bramble species are important because they provide foraging and nesting habitats for numerous vertebrates and invertebrates. It is recommended to include the apomict Rubus species in biodiversity accounts, for instance in the national standard list of plant species, as well as the Red List.

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
Blin, Kai ; Medema, M.H. ; Kottmann, Renzo ; Lee, Sang Yup ; Weber, Tilmann - \ 2016
Nucleic Acids Research 45 (2016)D1. - ISSN 0305-1048 - p. D555 - D559.
Secondary metabolites produced by microorganisms are the main source of bioactive compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and pesticides. In the last decade, the increasing availability of microbial genomes has established genome mining as a very important method for the identification of their biosynthetic gene clusters (BGCs). One of the most popular tools for this task is antiSMASH. However, so far, antiSMASH is limited to de novo computing results for user-submitted genomes and only partially connects these with BGCs from other organisms. Therefore, we developed the antiSMASH database, a simple but highly useful new resource to browse antiSMASH-annotated BGCs in the currently 3907 bacterial genomes in the database and perform advanced search queries combining multiple search criteria. antiSMASH-DB is available at http://antismash-db.secondarymetabolites.org/.
Ultra-Fast Fluorescence Anisotropy Decay of N-Acetyl-l-Tryptophanamide Reports on the Apparent Microscopic Viscosity of Aqueous Solutions of Guanidine Hydrochloride
Visser, A.J.W.G. ; Visser, N.V. ; Hoek, A. van; Amerongen, H. van - \ 2016
In: Perspectives on Fluorescence / Jameson, D.M., Switzerland : Springer (Springer Series on Fluorescence ) - ISBN 9783319413266 - p. 81 - 94.
The very fast fluorescence anisotropy decay of N-acetyl-l-tryptophanamide (NATA) in aqueous solutions has been measured with sub-picosecond laser excitation and detection with time-correlated single photon counting. By using global analysis of both parallel and perpendicular polarized fluorescence intensity decays involving deconvolution, the rotational correlation times of NATA in the tens of picosecond range are accurately recovered. Since rotational correlation times are directly proportional to viscosity, we have used these correlation times to derive the (relative) microscopic viscosity of increasing concentrations of guanidine hydrochloride (GuHCl) in buffered water. GuHCl is a well-known chaotropic agent of protein denaturation. We give a step-by-step description how to obtain the final results. Subsequently, we compare the obtained microscopic viscosities with macroscopic viscosity data reported half a century ago using capillary viscosimeters. From the results it is clear that GuHCl, present in molar concentration, associates with NATA making the apparent molecular volume larger.
Daytime formation of nitrous acid at a coastal remote site in Cyprus indicating a common ground source of atmospheric HONO and NO
Meusel, Hannah ; Kuhn, Uwe ; Reiffs, Andreas ; Mallik, Chinmay ; Harder, Hartwig ; Martinez, Monica ; Schuladen, Jan ; Bohn, Birger ; Parchatka, Uwe ; Crowley, John N. ; Fischer, Horst ; Tomsche, Laura ; Novelli, Anna ; Hoffmann, Thorsten ; Janssen, Ruud H.H. ; Hartogensis, Oscar ; Pikridas, Michael ; Vrekoussis, Mihalis ; Bourtsoukidis, Efstratios ; Weber, Bettina ; Lelieveld, Jos ; Williams, Jonathan ; Pöschl, Ulrich ; Cheng, Yafang ; Su, Hang - \ 2016
Atmospheric Chemistry and Physics 16 (2016)22. - ISSN 1680-7316 - p. 14475 - 14493.

Characterization of daytime sources of nitrous acid (HONO) is crucial to understand atmospheric oxidation and radical cycling in the planetary boundary layer. HONO and numerous other atmospheric trace constituents were measured on the Mediterranean island of Cyprus during the CYPHEX (Cyprus PHotochemical EXperiment) campaign in summer 2014. Average volume mixing ratios of HONO were 35 pptv (±25 pptv) with a HONO/NOx ratio of 0.33, which was considerably higher than reported for most other rural and urban regions. Diel profiles of HONO showed peak values in the late morning (60 ± 28 pptv around 09:00 local time) and persistently high mixing ratios during daytime (45 ± 18 pptv), indicating that the photolytic loss of HONO is compensated by a strong daytime source. Budget analyses revealed unidentified sources producing up to 3.4 × 106 molecules cm-3 s-1 of HONO and up to 2.0 × 107 molecules cm-3 s-1 NO. Under humid conditions (relative humidity 2 Combining double low line 0.72), suggesting a common source that may be attributable to emissions from microbial communities on soil surfaces.

Unearthing the transition rates between photoreceptor conformers
Smith, Robert W. ; Helwig, Britta ; Westphal, Adrie H. ; Pel, Eran ; Hörner, Maximilian ; Beyer, Hannes M. ; Samodelov, Sophia L. ; Weber, Wilfried ; Zurbriggen, Matias D. ; Borst, Janwillem ; Fleck, Christian - \ 2016
BMC Systems Biology 10 (2016)1. - ISSN 1752-0509
Optimisation - Optogenetics - Photoconversion - Phytochromes

Background: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (P A ) and inactive (P I ) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions. Results: Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools. Conclusions: The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained.

Aerial low-frequency hearing in captive and free-ranging harbour seals (Phoca vitulina) measured using auditory brainstem responses
Lucke, K. ; Hastie, Gordon D. ; Ternes, Kerstin ; McConnell, Bernie ; Moss, Simon ; Russell, Deborah J.F. ; Weber, Heike ; Janik, Vincent M. - \ 2016
Journal of Comparative Physiology A-Sensory Neural and Behavioral Physiology 202 (2016)12. - ISSN 0340-7594 - p. 859 - 868.
ABR - Harbour seal - Hearing - Low frequency - Phoca vitulina

The hearing sensitivity of 18 free-ranging and 10 captive harbour seals (Phoca vitulina) to aerial sounds was measured in the presence of typical environmental noise through auditory brainstem response measurements. A focus was put on the comparative hearing sensitivity at low frequencies. Low- and mid-frequency thresholds appeared to be elevated in both captive and free-ranging seals, but this is likely due to masking effects and limitations of the methodology used. The data also showed individual variability in hearing sensitivity with probable age-related hearing loss found in two old harbour seals. These results suggest that the acoustic sensitivity of free-ranging animals was not negatively affected by the soundscape they experienced in the wild.

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