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    Planning for citizen participation in the EU mission to restore our ocean and waters by 2030
    (Springer, 2024-09-26) Whyte, David; Debaveye, Line; Bjørkan, Maiken; Steiro, Vida Maria Daae; Maria Vittoria Marra; Seys, Jan; Deane, Aoife; Namisnik, Wendy; Pelegri, Josep L.; Simon, Carine; Falcieri, Francesco; Giuffredi, Rita; Laurenza, Lucia; Apazoglou, Eirini; Petersen, H. Cecilie; Carbajal, María Elena; Giannoukakou-Leontsini, Ifigeneia; Fuster, Noemí; Nys, Cécile; HORIZON EUROPE Framework Programme
    The European Commission’s Mission to “Restore our Ocean and Waters by 2030” (Mission Ocean & Waters) is, at the most superficial level, an overarching policy framework with the primary aim of improving the health of European ocean, sea, and freshwater ecosystems. However, its use of the Mission framing and emphasis on fostering social, political, and economic transformations through its activities makes it a much more holistic and ambitious undertaking. This article explores challenges and opportunities that arise with the emphasis placed on increasing citizen participation in Mission Ocean & Waters, in the context of “Post-Normal Science” (Funtowicz & Ravetz Funtowicz and Ravetz, Krimsky and Golding (eds), Social Theories of Risk, Greenwood Press, Westport, 1992). We begin with a description of Mission Ocean & Waters, discussing its citizen engagement ambitions through the lens of Post-Normal Science, before describing the research methods used by the Horizon Europe project Preparing the Research and Innovation Core for Mission Oceans, Seas, & Waters (PREP4BLUE). We then present our results, highlighting four citizen engagement-based challenges that the Mission faces, and how PREP4BLUE has engaged with them. Finally, we discuss the future activities or structural changes that will be required if the Mission’s citizen engagement targets are to be achieved and for citizens to become core actors in protecting European aquatic ecosystems and developing a sustainable blue economy. These insights should prove useful to those developing and delivering Mission projects and those researching citizen participation in ocean and freshwater related challenges.
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    Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus
    (Oxford University Press, 2022) Fenton, Darren; Kiniry, Stephen J.; Yordanova, Martina M.; Baranov, Pavel V.; Morrissey, John P.; Horizon 2020 Framework Programme; Science Foundation Ireland; Health Research Board; Wellcome Trust
    Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.
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    Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
    (Springer Nature, 2022) Domenzain, Ivan; Sánchez, Benjamín; Anton, Mihail; Kerkhoven, Eduard J.; Millan-Oropeza, Aaron; Henry, Celine; Siewers, Verena; Morrissey, John P.; Sonnenschein, Nikolaus; Nielsen, Jens; Horizon 2020 Framework Programme; Knut och Alice Wallenbergs Stiftelse; Novo Nordisk Fonden
    Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.
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    Integration of non-target metabolomics and sensory analysis unravels vegetable plant metabolite signatures associated with sensory quality: a case study using dill (Anethum graveolens)
    (Elsevier, 2021) Castro-Alves, Victor; Kalbina, Irina; Nilsen, Asgeir; Aronsson, Mats; Rosenqvist, Eva; Jansen, Marcel A. K.; Qian, Minjie; Öström, Åsa; Hyötyläinen, Tuulia; Strid, Åke; Knowledge Foundation; Svenska Forskningsrådet Formas
    Using dill (Anethum graveolens L.) as a model herb, we reveal novel associations between metabolite profile and sensory quality, by integrating non-target metabolomics with sensory data. Low night temperatures and exposure to UV-enriched light was used to modulate plant metabolism, thereby improving sensory quality. Plant age is a crucial factor associated with accumulation of dill ether and α-phellandrene, volatile compounds associated with dill flavour. However, sensory analysis showed that neither of these compounds has any strong association with dill taste. Rather, amino acids alanine, phenylalanine, glutamic acid, valine, and leucine increased in samples exposed to eustress and were positively associated with dill and sour taste. Increases in amino acids and organic acids changed the taste from lemon/grass to a more bitter/pungent dill-related taste. Our procedure reveals a novel approach to establish links between effects of eustressors on sensory quality and may be applicable to a broad range of crops.
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    A taxonomic revision of Lemna sect. Uninerves (Lemnaceae)
    (John Wiley and Sons Inc., 2020) Bog, Manuela; Sree, K. Sowjanya; Fuchs, Joerg; Hoang, Phuong T.N.; Schubert, Ingo; Kuever, Jan; Rabenstein, Andreas; Paolacci, Simona; Jansen, Marcel A. K.; Appenroth, Klaus-J.; Deutsche Forschungsgemeinschaft
    Lemna sect. Uninerves Hegelm. consists of three species, Lemna minuta Kunth (synonym L. minuscula), L. valdiviana Phil. and L. yungensis Landolt. Lemna yungensis was discovered growing on rocks in the Yungas in Bolivia by E. Landolt and was described just 20 years ago. In the original description, Landolt reported that this species is closely related to L. valdiviana and that it is difficult to distinguish the three species on a morphological basis. Therefore, the taxonomic position and status of L. yungensis remained controversial. Here, we carried out a detailed taxonomic study, integrating approaches that include quantitative morphometry, metabolomic profiling by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) as well as molecular genetic analysis using amplified fragment length polymorphism (AFLP), and barcoding of plastidic sequences. We also investigated genome sizes of clones of the three species. Whereas L. minuta can easily be differentiated from L. valdiviana and L. yungensis, it was not possible to distinguish L. valdiviana from L. yungensis with any of the methods used. These data imply that L. yungensis is identical to L. valdiviana. Thus, the name L. yungensis should be synonymised with the name L. valdiviana, since this is the older name.