1201. Enabling reusability of plant phenomic datasets with MIAPPE 1.1Evangelia A. Papoutsoglou, Daniel Faria, Daniel Arend, Elizabeth Arnaud, Ioannis N. Athanasiadis, Inês Chaves, Frederik Coppens, Guillaume Cornut, Bruno V. Costa, Hanna Ćwiek-Kupczyńska, Kristina Gruden, Živa Ramšak, 2020, original scientific article Abstract: Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity.
We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples.
We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0.
MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
Published in DiRROS: 22.07.2024; Views: 237; Downloads: 227
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1202. A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmlandLorna J. Cole, David Kleijn, Lynn Dicks, Jane C. Stout, Simon G. Potts, Matthias Albrecht, Mario V. Balzan, Ignasi Bartomeus, Penelope J. Bebeli, Danilo Bevk, Jacobus C. Biesmeijer, Robert Chlebo, Anželika Dautarte, Nikolaos Emmanouil, Chris Hartfield, John M. Holland, Andrea Holzschuh, Nieke T. J. Knoben, Anikó Kovács-Hostyánszki, Yael Mandelik, Heleni Panou, Robert J. Paxton, Theodora Petanidou, Miguel A.A. Pinheiro de Carvalho, Maj Rundlöf, Jean-Pierre Sarthou, Menelaos C. Stavrinides, Maria Jose Suso, Hajnalka Szentgyörgyi, Bernard E. Vaissière, Androulla Varnava, Vilà Montserrat, Romualdas Zemeckis, Jeroen Scheper, 2020, original scientific article Abstract: Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in their potential to support insect pollinators under standard and pollinator-friendly management, as well as the extent of farmer uptake.
A structured Delphi elicitation process engaged 22 experts from 18 European countries to evaluate EFAs options. By considering life cycle requirements of key pollinating taxa (i.e. bumble bees, solitary bees and hoverflies), each option was evaluated for its potential to provide forage, bee nesting sites and hoverfly larval resources.
EFA options varied substantially in the resources they were perceived to provide and their effectiveness varied geographically and temporally. For example, field margins provide relatively good forage throughout the season in Southern and Eastern Europe but lacked early-season forage in Northern and Western Europe. Under standard management, no single EFA option achieved high scores across resource categories and a scarcity of late season forage was perceived.
Experts identified substantial opportunities to improve habitat quality by adopting pollinator-friendly management. Improving management alone was, however, unlikely to ensure that all pollinator resource requirements were met. Our analyses suggest that a combination of poor management, differences in the inherent pollinator habitat quality and uptake bias towards catch crops and nitrogen-fixing crops severely limit the potential of EFAs to support pollinators in European agricultural landscapes.
Policy Implications. To conserve pollinators and help protect pollination services, our expert elicitation highlights the need to create a variety of interconnected, well-managed habitats that complement each other in the resources they offer. To achieve this the Common Agricultural Policy post-2020 should take a holistic view to implementation that integrates the different delivery vehicles aimed at protecting biodiversity (e.g. enhanced conditionality, eco-schemes and agri-environment and climate measures). To improve habitat quality we recommend an effective monitoring framework with target-orientated indicators and to facilitate the spatial targeting of options collaboration between land managers should be incentivised.
Keywords: agri-environment schemes, bees, CAP Green Architecture, Common Agricultural Policy, Ecological Focus Areas, habitat complementarity, pollination services, pollinator conservation
Published in DiRROS: 22.07.2024; Views: 311; Downloads: 319
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1203. A marine biodiversity observation network for genetic monitoring of hard-bottom communities (ARMS-MBON)Matthias Obst, Katrina Exter, A. Louise Allcock, Christos Arvanitidis, Alizz Axberg, Maria Bustamante, Ana Fortič, Borut Mavrič, Andreja Ramšak, 2020, original scientific article Abstract: Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre (www.embrc.eu).
Keywords: benthic invertebrates, Marine Strategy Framework Directive (MSFD), Essential Biodiversity Variables (EBVs), Essential Ocean Variables (EOVs), European Marine Biological Resource Centre (EMBRC), non-indigenous species (NIS), genomic observatories, marine biodiversity assessment
Published in DiRROS: 22.07.2024; Views: 320; Downloads: 221
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1204. Characterization of In vitro 3D cell model developed from human hepatocellular carcinoma (HepG2) cell lineMartina Štampar, Barbara Breznik, Metka Filipič, Bojana Žegura, 2020, original scientific article Abstract: In genetic toxicology, there is a trend against the increased use of in vivo models as highlighted by the 3R strategy, thus encouraging the development and implementation of alternative models. Two-dimensional (2D) hepatic cell models, which are generally used for studying the adverse effects of chemicals and consumer products, are prone to giving misleading results. On the other hand, newly developed hepatic three-dimensional (3D) cell models provide an attractive alternative, which, due to improved cell interactions and a higher level of liver-specific functions, including metabolic enzymes, reflect in vivo conditions more accurately. We developed an in vitro 3D cell model from the human hepatocellular carcinoma (HepG2) cell line. The spheroids were cultured under static conditions and characterised by monitoring their growth, morphology, and cell viability during the time of cultivation. A time-dependent suppression of cell division was observed. Cell cycle analysis showed time-dependent accumulation of cells in the G0/G1 phase. Moreover, time-dependent downregulation of proliferation markers was shown at the mRNA level. Genes encoding hepatic markers, metabolic phase I/II enzymes, were time-dependently deregulated compared to monolayers. New knowledge on the characteristics of the 3D cell model is of great importance for its further development and application in the safety assessment of chemicals, food products, and complex mixtures.
Published in DiRROS: 22.07.2024; Views: 252; Downloads: 196
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1205. New alien Mediterranean biodiversity records (October 2020)Michail Ragkousis, Nardjes Abdelali, Ernesto Azzurro, Ali Badreddine, Michel Bariche, Ghazi Bitar, Fabio Crocetta, Francesco Denitto, Ana Fortič, Borut Mavrič, 2020, original scientific article Abstract: This article includes 23 new records of alien and cryptogenic species in the Mediterranean Sea, belonging to 4 Phyla (Chordata, Echinodermata, Arthropoda and Mollusca), distributed from the Alboran to the Levantine Sea. Records are reported from eight countries listed from West to East as follows: Algeria: new records of the Atlantic blue crab Callinectes sapidus; Spain: further spread and establishment of the sea slug Lamprohaminoea ovalis in continental shores; Tunisia: first record of the Atlantic Blue Crab Callinectes sapidus in the Gulf of Gabes; Italy: a new occurrence of the pufferfish Lagocephalus sceleratus in Northern Ionian waters; first record of Cephalopholis taeniops in the Ionian Sea; first record of the redlip blenny, Ophioblennius atlanticus in the Ionian Sea; Slovenia: first record of the isopod Paranthura japonica in Slovenia; Greece: first record of the molluscs Eunaticina papilla, Plocamopherus ocellatus and the fish Cheilodipterus novemstriatus; first record of the ascidian Ecteinascidia turbinata in Kriti; the long-spined sea urchin Diadema setosum in the Ionian Sea; Turkey: first record of the sea spider Ammothea hilgendorfi; the stomatopod Cloridina cf. ichneumon; the fishes Pempheris rhomboidea from the Sea of Marmara and Paranthias furcifer from the Aegean Sea; Lebanon: new records of the fishes Arothron hispidus, Rachycentron canadum, Heniochus intermedius and Acanthurus monroviae; first record of Acanthostracion polygonius. The records of Cloridina cf. ichneumon from southern Turkey and the fish Acanthostracion polygonius from Lebanon, both being the first Mediterranean records, are noteworthy.
Published in DiRROS: 22.07.2024; Views: 433; Downloads: 215
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1206. Minimum Information for Reporting on the Comet Assay (MIRCA) : recommendations for describing comet assay procedures and resultsPeter Møller, Amaya Azqueta, Elisa Boutet-Robinet, Gudrun Koppen, Stefano Bonassi, Mirta Milić, Goran Gajski, Solange Costa, Bojana Žegura, Matjaž Novak, 2020, original scientific article Abstract: The comet assay is a widely used test for the detection of DNA damage and repair activity. However, there are interlaboratory differences in reported levels of baseline and induced damage in the same experimental systems. These differences may be attributed to protocol differences, although it is difficult to identify the relevant conditions because detailed comet assay procedures are not always published. Here, we present a Consensus Statement for the Minimum Information for Reporting Comet Assay (MIRCA) providing recommendations for describing comet assay conditions and results. These recommendations differentiate between ‘desirable’ and ‘essential’ information: ‘essential’ information refers to the precise details that are necessary to assess the quality of the experimental work, whereas ‘desirable’ information relates to technical issues that might be encountered when repeating the experiments. Adherence to MIRCA recommendations should ensure that comet assay results can be easily interpreted and independently verified by other researchers.
Published in DiRROS: 22.07.2024; Views: 308; Downloads: 205
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1207. Heavy metals in the Adriatic-Ionian Seas : a case study to illustrate the challenges in data management when dealing with regional datasetsMaria-Eugenia Molina Jack, Rigers Bakiu, Ana Castelli, Branko Čermelj, Maja Fafanđel, Christina Georgopoulou, Giordano Giorgi, Athanassia Iona, Damir Ivankovic, Martina Kralj, Elena Partescano, Alice Rotini, Melita Velikonja, Marina Lipizer, 2020, original scientific article Abstract: Harmonization of monitoring protocols and analytical methods is a crucial issue for transnational marine environmental status assessment, yet not the only one. Coherent data management and quality control become very relevant when environmental status is assessed at regional or subregional scale (e.g., for the Mediterranean or the Adriatic Sea), thus requiring data from different sources. Heavy metals are among the main targets of monitoring activities. Significant efforts have been dedicated to share best practices for monitoring and assessment of ecosystem status and to strengthen the network of national, regional and European large data infrastructures in order to facilitate the access to data among countries. Data comparability and interoperability depend not only on sampling and analytical protocols but also on how data and metadata are managed, quality controlled and made accessible. Interoperability is guaranteed by using common metadata and data formats, and standard vocabularies to assure homogeneous syntax and semantics. Data management of contaminants is complex and challenging due to the high number of information required on sampling and analytical procedures, high heterogeneity in matrix characteristics, but also to the large and increasing number of pollutants. Procedures for quality control on heterogeneous datasets provided by multiple sources are not yet uniform and consolidated. Additional knowledge and reliable long time-series of data are needed to evaluate typical ranges of contaminant concentration. The analysis of a coherent and harmonized regional dataset can provide the basis for a multi-step quality control procedure, which can be further improved as knowledge increases during data validation process.
Keywords: contaminants, data management, harmonization, Adriatic Sea, Ionian Sea, pollution, assessment, heavy metals
Published in DiRROS: 22.07.2024; Views: 348; Downloads: 228
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1208. Chocolate and risk of chronic disease : a systematic review and dose-response meta-analysisJakub Morze, Carolina Schwedhelm, Aleksander Benčič, Georg Hofmann, Heiner Boeing, Katarzyna Przybylowicz, Lukas Schwingshackl, 2020, original scientific article Abstract: Purpose
Evidence for the association between chocolate intake and risk of chronic diseases is inconclusive. Therefore, we aimed to synthesize and evaluate the credibility of evidence on the dose-response association between chocolate consumption with risk of all-cause mortality, coronary heart disease (CHD), stroke, heart failure (HF), type 2 diabetes (T2D), colorectal cancer (CRC), and hypertension.
Methods
Prospective studies were searched until July 2018 in PubMed, Embase, and Web of Science. Random-effects meta-analyses comparing highest versus lowest intake categories, linear, and non-linear dose-response analyses were conducted. The credibility of evidence was evaluated with the NutriGrade scoring-system.
Results
Overall, 27 investigations were identified (n = 2 for all-cause mortality, n = 9 for CHD, n = 8 for stroke, n = 6 for HF, n = 6 for T2D, n = 2 for hypertension and CRC, respectively). No associations with HF (RR 0.99, 95% CI 0.94, 1.04) and T2D (RR 0.94, 95% CI 0.88, 1.01) per each 10 g/day increase in chocolate intake were observed in the linear dose-response meta-analyses. However, a small inverse association for each 10 g/daily increase could be shown for the risk of CHD (RR 0.96, 95% CI 0.93, 0.99), and stroke (RR 0.90, 95% CI 0.82, 0.98). The credibility of evidence was rated either very low (all-cause mortality, HF, T2D, CRC or hypertension) or low (CHD, stroke).
Conclusion
Chocolate consumption is not related to risk for several chronic diseases, but could have a small inverse association with CHD and stroke. Our findings are limited by very low or low credibility of evidence, highlighting important uncertainty for chocolate–disease associations.
Keywords: chocolate, meta-analysis, dose-response, credibility of evidence, chronic diseases
Published in DiRROS: 22.07.2024; Views: 269; Downloads: 198
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1209. Microbial processing of jellyfish detritus in the oceanTinkara Tinta, Zihao Zhao, Alvaro Escobar, Katja Klun, Barbara Bayer, Chie Amano, Luca Bamonti, Gerhard J. Herndl, 2020, original scientific article Abstract: When jellyfish blooms decay, sinking jellyfish detrital organic matter (jelly-OM), rich in proteins and characterized by a low C:N ratio, becomes a significant source of OM for marine microorganisms. Yet, the key players and the process of microbial jelly-OM degradation and the consequences for marine ecosystems remain unclear. We simulated the scenario potentially experienced by the coastal pelagic microbiome after the decay of a bloom of the cosmopolitan Aurelia aurita s.l. We show that about half of the jelly-OM is instantly available as dissolved organic matter and thus, exclusively and readily accessible to microbes. During a typical decay of an A. aurita bloom in the northern Adriatic Sea about 100 mg of jelly-OM L–1 becomes available, about 44 μmol L–1 as dissolved organic carbon (DOC), 13 μmol L–1 as total dissolved nitrogen, 11 μmol L–1 of total hydrolyzable dissolved amino acids (THDAA) and 0.6 μmol L–1 PO43–. The labile jelly-OM was degraded within 1.5 days (>98% of proteins, ∼70% of THDAA, 97% of dissolved free amino acids and the entire jelly-DOC pool) by a consortium of Pseudoalteromonas, Alteromonas, and Vibrio. These bacteria accounted for >90% of all metabolically active jelly-OM degraders, exhibiting high bacterial growth efficiencies. This implies that a major fraction of the detrital jelly-OM is rapidly incorporated into biomass by opportunistic bacteria. Microbial processing of jelly-OM resulted in the accumulation of tryptophan, dissolved combined amino acids and inorganic nutrients, with possible implications for biogeochemical cycles.
Published in DiRROS: 22.07.2024; Views: 309; Downloads: 218
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1210. COVID-19 pandemic consequences on coastal water quality using WST Sentinel-3 Data : case of Tangier, MoroccoEl Khalil Cherif, Martin Vodopivec, Nezha Mejjad, Joaquim C.G Esteves da Silva, Simona Simonovič, Hakim Boulaassal, 2020, original scientific article Abstract: The west coast of Tangier, in northern Morocco, has been affected by industrial wastewater discharge that reaches the ocean through the Boukhalef river. Therefore, the Jbila and Sidikacem beaches near to the Boukhalef river mouth have been classified as polluted for many years. With the aim of determining the COVID-19 pandemic consequences on the Tangier coastal environment, a linear model using Sentinel 3 water surface temperature (WST) has been tested in several locations. Data from April 2019 and April 2020, before and during the COVID-19 pandemic related emergency status in Morocco, were compared. The results from April 2019 showed high WST values and consequently, the poorest water quality in the sites closest to the Boukhalef river mouth. On the other hand, the results from April 2020 showed normal WST values and high water quality in the same study area. These results illustrate the usefulness of Sentinel 3 WST for the estimation of bathing water quality on the west coast of Tangier. The study shows the positive impact of the COVID-19 pandemic consequences on the coastal environment quality in the study area and indicates the importance of decreasing the industrial discharge on the west coast of Tangier. The same methodology could be used in decision-making processes and to reduce cost, time and human resources for coastal monitoring systems. We demonstrate the potential of using the Sentinel 3 data for coastal waters monitoring, as well as the need for stricter controls of pollutant discharges into the world’s rivers.
Keywords: COVID-19, Sentinel 3, WST, Tangier west coast, coastal waters, bathing waters, industrial activities
Published in DiRROS: 22.07.2024; Views: 298; Downloads: 211
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