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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    The Global Invertebrate Genomics Alliance (GIGA). 2014. Developing Community Resources to Study Diverse Invertebrate Genomes
    Pomponi, S.A. - \ 2014
    Journal of Heredity 105 (2014)1. - ISSN 0022-1503 - p. 1 - 18.
    marine natural-products - gene-expression - draft genome - tetranychus-urticae - human microbiome - whole-genome - fresh-water - evolution - phylogeny - coral
    Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness.
    Cultivation of Sponges, Sponge Cells and Symbionts: Achievements and Future Prospects
    Schippers, K.J. ; Sipkema, D. ; Osinga, R. ; Smidt, H. ; Pomponi, S.A. ; Martens, D.E. ; Wijffels, R.H. - \ 2012
    Advances in Marine Biology 62 (2012). - ISSN 0065-2881 - p. 273 - 337.
    marine natural-products - fresh-water sponge - biologically-active metabolites - chondrosia-reniformis nardo - petrosia-ficiformis poiret - ex-situ cultivation - organic-carbon doc - in-vitro - aplysina-aerophoba - secondary metabolites
    Marine sponges are a rich source of bioactive compounds with pharmaceutical potential. Since biological production is one option to supply materials for early drug development, the main challenge is to establish generic techniques for small-scale production of marine organisms. We analysed the state of the art for cultivation of whole sponges, sponge cells and sponge symbionts. To date, cultivation of whole sponges has been most successful in situ; however, optimal conditions are species specific. The establishment of sponge cell lines has been limited by the inability to obtain an axenic inoculum as well as the lack of knowledge on nutritional requirements in vitro. Approaches to overcome these bottlenecks, including transformation of sponge cells and using media based on yolk, are elaborated. Although a number of bioactive metabolite-producing microorganisms have been isolated from sponges, and it has been suggested that the source of most sponge-derived bioactive compounds is microbial symbionts, cultivation of sponge-specific microorganisms has had limited success. The current genomics revolution provides novel approaches to cultivate these microorganisms
    Towards Commercial Production of Sponge Medicines
    Koopmans, M. ; Martens, D.E. ; Wijffels, R.H. - \ 2009
    Marine Drugs 7 (2009)4. - ISSN 1660-3397 - p. 787 - 802.
    biologically-active metabolites - antimalarial-drug precursor - marine natural-products - secondary metabolites - aplysina-aerophoba - chemical defenses - sustainable production - bioactive metabolites - caribbean sponges - cellular-origin
    Sponges can provide potential drugs against many major world-wide occurring diseases. Despite the high potential of sponge derived drugs no sustainable production method has been developed. Thus far it is not fully understood why, when, where and how these metabolites are produced in sponges. For the near future sea-based sponge culture seems to be the best production method. However, for controlled production in a defined system it is better to develop in vitro production methods, like in vitro sponge culture or even better sponge cell culture, culture methods for symbionts or the transfer of production routes into another host. We still have insufficient information about the background of metabolite production in sponges. Before production methods are developed we should first focus on factors that can induce metabolite production. This could be done in the natural habitat by studying the relation between stress factors (such as predation) and the production of bioactive metabolites. The location of production within the sponge should be identified in order to choose between sponge cell culture and symbiont culture. Alternatively the biosynthetic pathways could be introduced into hosts that can be cultured. For this the biosynthetic pathway of metabolite production should be unraveled, as well as the genes involved. This review discusses the current state of sponge metabolite production and the steps that need to be taken to develop commercial production techniques. The different possible production techniques are also discussed
    Hypothesized kinetic models for describing the growth of globular and encrusting demosponges
    Sipkema, D. ; Yosef, N.A.M. ; Adamczewski, M. ; Osinga, R. ; Mendola, D. ; Tramper, J. ; Wijffels, R.H. - \ 2006
    Marine Biotechnology 8 (2006)1. - ISSN 1436-2228 - p. 40 - 51.
    marine natural-products - dissolved organic-carbon - sponge crambe-crambe - culture - dynamics - metabolites - aquaculture - explants - sea
    The marine sponges Dysidea avara and Chondrosia reniformis (globular forms) were cultured in the laboratory on a diet of viable Phaeodactylum tricornutum cells and dissolved nutrients (algae and fish powders). Our growth data were combined with literature data for Pseudosuberites andrewsi (a globular sponge) and for the encrusting sponges Oscarella lobularis, Hemimycale columella, and Crambe crambe. The suitability of three growth models-linear, exponential, and radial accretive-for describing the growth of globular and encrusting sponges was assessed. Radial accretive growth was determined to be the best model to describe growth of both encrusting and globular sponges. Average growth rates of 0.051 ± 0.016 and 0.019 ± 0.003 mm/day (calculated as the increase of the radius of the sponge per day) were obtained experimentally for D. avara and C. reniformis, respectively
    Occurrence, biological activity and synthesis of drimane sesquiterpenoids
    Jansen, B.J.M. ; Groot, Æ. de - \ 2004
    Natural Product Reports 21 (2004)4. - ISSN 0265-0568 - p. 449 - 477.
    nudibranch cadlina-luteomarginata - fungus cryptoporus-volvatus - neuroblastoma sh-sy5y cells - s-alkoxycarbonyl xanthates - receptor-binding activity - ganoderma-neo-japonicum - gastric-mucosal lesions - marine natural-products - pieris-brassicae larvae - diels-a
    In this review the names, structures and occurrence of all new drimanes and rearranged drimanes, which have been published between January 1990 and January 2003 have been collected. Subjects that have been treated are biosynthesis, analysis, biological activities, with special attention to cytotoxic activity and antifeedant and insecticidal activity and mode of action. An important part of the review deals with the synthesis of drimanes. This part has been subdivided into syntheses by transformation of natural products, syntheses starting from chiral compounds obtained by enzymatic resolution, syntheses by cationic polyolefin cyclizations, syntheses from trans-decalones, syntheses by radical cyclizations and syntheses by cycloaddition reactions. The review contains about 350 references.
    The life and death of sponge cells
    Sipkema, D. ; Snijders, A.P.L. ; Schroën, C.G.P.H. ; Osinga, R. ; Wijffels, R.H. - \ 2004
    Biotechnology and Bioengineering 85 (2004)3. - ISSN 0006-3592 - p. 239 - 247.
    marine natural-products - in-vitro - growth-inhibition - primary culture - ammonium ion - heat-stress - trehalose - sea - identification - cytotoxicity
    Cell viability is an essential touchstone in the study of the effect of medium components on cell physiology. We developed a flow-cytometric assay to determine sponge-cell viability, based on the combined use of fluorescein diacetate (FDA) and propidium iodide (PI). Cell fluorescence measurements based on incubation of cells with FDA or PI resulted in a useful and reproducible estimate of the viability of primary sponge-cell cultures. We studied the effects of temperature, ammonium, and the fungicide amphotericin B on the viability of a primary-cell culture from the marine sponge Suberites domuncula using the aforementioned flow-cytometric assay. S. domuncula cells die rapidly at a temperature of greater than or equal to22degreesC, but they are insensitive to ammonium concentrations of up to 25 mM. Amphotericin B, which is frequently used in sponge-cell culture media, was found to be toxic to S. domuncula cells. (C) 2004 Wiley Periodicals, Inc.
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