1. New tools and recommendations for a better management of harmful algal blooms under the European Marine Strategy Framework DirectiveYolanda Sagarmínaga, Esther Garcés, Janja Francé, Rowena Stern, Marta Revilla, Erika Magaletti, Eileen Bresnan, George Tsirtsis, 2023, pregledni znanstveni članek Povzetek: Marine harmful algal blooms (HABs), caused by various aquatic microalgae, pose significant risks to ecosystems, some socio-economic activities and human health. Traditionally managed as a public health issue through reactive control measures such as beach closures, seafood trade bans or closure of mollusc production areas, the multifaceted linkages of HABs with environmental and socio-economic factors require more comprehensive ecosystem-based management approach tools to support policies. This study promotes a coordinated understanding and implementation of HAB assessment and management under the Marine Strategy Framework Directive (MSFD), targeting the achievement of Good Environmental Status (GES) in European marine waters. We introduce two novel tools: GES4HABs (GES for HABs) decision tree, and MAMBO (environMental mAtrix for the Management of BlOoms), a decision support matrix. These tools aim to streamline HABs reporting and prioritize resource allocation and management interventions. The GES4HABs decision tree defines a sequence of decision steps to identify HAB management strategies according to their state (evaluated against predefined baselines) and causes (anthropic or natural). MAMBO is proposed to address different HABs and their interaction with human and environmental pressures. The matrix utilizes two axes: natural trophic status and level of human influence, capturing major aspects such as nutrient supply. While acknowledging the limitations of this simplified framework, MAMBO categorizes marine regions into quadrants of varying management viability. Regions with high human influence and eutrophic conditions are identified as most suitable for effective management intervention, whereas regions with minimal or mixed human influence are deemed less amenable to active management. In addition, we explore and describe various indicators, monitoring methods and initiatives that may be relevant to support assessments of HAB status and associated pressures and impacts in the MSFD reporting. Finally, we provide some recommendations to promote the consideration of HABs in ecosystem-based management strategies, intensify efforts for harmonizing and defining best practices of analysis, monitoring and assessment methodologies, and foster international and cross-sectoral coordination to optimize resources, efforts and roles.
Ključne besede: decision support tools, ecosystem-based management, indicators, marine monitoring, eutrophication, marine biotoxins, environmental assessment, pressures and impacts
Objavljeno v DiRROS: 05.08.2024; Ogledov: 50; Prenosov: 82
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2. Extraction of DNA from different sample types - a practical approach for GMO testingJana Žel, Tina Demšar, Dejan Štebih, Mojca Milavec, Kristina Gruden, 2015, izvirni znanstveni članek Povzetek: Current methods based on DNA targets for the detection, identification and quantification of genetically modified organisms (GMOs) involve extraction of the DNA. Different extraction procedures have been developed for the great variety
of samples from food, feed, seeds and particular plant parts. This makes the operation of routine analytical laboratories complex and workloads heavy. Here we present a decision-making system, developed over many years of GMO testing on different samples, that result in the application of only a few extraction methods for the majority of samples. Developed decision-making system enables quicker and more cost effective testing of GMOs. In addition, the performance of DNA extraction resulting from the use of the selected extraction methods is presented for use in subsequent testing of GMOs by real time PCR methods. This approach can be used as a model for similar systems based on nucleic acid analysis in food, feed, seeds and plants.
Ključne besede: extraction methods, genetically modified organisms, GMO, decision- making system (biology), GMO testing, cetyltrimethylammonium bromide, CTAB
Objavljeno v DiRROS: 29.07.2024; Ogledov: 86; Prenosov: 69
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3. quantGenius : implementation of a decision support system for qPCR-based gene quantificationŠpela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe Novak, Kristina Gruden, 2017, izvirni znanstveni članek Povzetek: Background
Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification.
Results
We have developed “quantGenius” (http://quantgenius.nib.si), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry–independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases.
Conclusions
To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.
Ključne besede: quantitative molecular biology, quantitative PCR, nucleic acid quantification, web application, decision support system
Objavljeno v DiRROS: 24.07.2024; Ogledov: 101; Prenosov: 109
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4. Decision support for the comparative evaluation and selection of analytical methods : detection of genetically modified organisms as an exampleDavid Dobnik, Kristina Gruden, Jana Žel, Yves Bertheau, Arne Holst-Jensen, Marko Bohanec, 2018, izvirni znanstveni članek Povzetek: The selection of the best-fit-for-purpose analytical method to be implemented in the laboratory is difficult due to availability of multiple methods, targets, aims of detection, and different kinds and sources of more or less reliable information. Several factors, such as method performance, practicability, cost of setup, and running costs need to be considered together with personnel training when selecting the most appropriate method. The aim of our work was to prepare a flexible multicriteria decision analysis model suitable for evaluation and comparison of analytical methods used for the purpose of detecting and/or quantifying genetically modified organisms, and to use this model to evaluate a variety of changing analytical methods. Our study included selection of PCR-, isothermal-, protein-, microarray-, and next-generation sequencing-based methods in simplex and/or multiplex formats. We show that the overall result of their fitness for purpose is relatively similar; however, individual criteria or a group of related criteria exposed more substantial differences between the methods. The proposed model of this decision support system enables easy modifications and is thus suitable for any other application of complex analytical methods.
Ključne besede: multicriteria decision analysis, genetically modified organisms, method evaluation, DEXi, decision support system, DSS
Objavljeno v DiRROS: 24.07.2024; Ogledov: 112; Prenosov: 136
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5. The LANDSUPPORT geospatial decision support system (S-DSS) vision : operational tools to implement sustainability policies in land planning and managementFabio Terribile, Marco Acutis, Antonella Agrillo, Erlisiana Anzalone, Sayed Azam-Ali, Marialaura Bancheri, Peter Baumann, Barbara Birli, Antonello Bonfante, Marco Botta, Mitja Ferlan, Jernej Jevšenak, Primož Simončič, Mitja Skudnik, 2023, izvirni znanstveni članek Povzetek: Nowadays, there is contrasting evidence between the ongoing continuing and widespread environmental degradation and the many means to implement environmental sustainability actions starting from good policies (e.g. EU New Green Deal, CAP), powerful technologies (e.g. new satellites, drones, IoT sensors), large databases and large stakeholder engagement (e.g. EIP-AGRI, living labs). Here, we argue that to tackle the above contrasting issues dealing with land degradation, it is very much required to develop and use friendly and freely available web-based operational tools to support both the implementation of environmental and agriculture policies and enable to take positive environmental sustainability actions by all stakeholders. Our solution is the S-DSS LANDSUPPORT platform, consisting of a free web-based smart Geospatial CyberInfrastructure containing 15 macro-tools (and more than 100 elementary tools), co-designed with different types of stakeholders and their different needs, dealing with sustainability in agriculture, forestry and spatial planning. LANDSUPPORT condenses many features into one system, the main ones of which were (i) Web-GIS facilities, connection with (ii) satellite data, (iii) Earth Critical Zone data and (iv) climate datasets including climate change and weather forecast data, (v) data cube technology enabling us to read/write when dealing with very large datasets (e.g. daily climatic data obtained in real time for any region in Europe), (vi) a large set of static and dynamic modelling engines (e.g. crop growth, water balance, rural integrity, etc.) allowing uncertainty analysis and what if modelling and (vii) HPC (both CPU and GPU) to run simulation modelling ‘on-the-fly’ in real time. Two case studies (a third case is reported in the Supplementary materials), with their results and stats, covering different regions and spatial extents and using three distinct operational tools all connected to lower land degradation processes (Crop growth, Machine Learning Forest Simulator and GeOC), are featured in this paper to highlight the platform's functioning. Landsupport is used by a large community of stakeholders and will remain operational, open and free long after the project ends. This position is rooted in the evidence showing that we need to leave these tools as open as possible and engage as much as possible with a large community of users to protect soils and land.
Ključne besede: land degradation, land management, soil, spatial decision support system, sustainability
Objavljeno v DiRROS: 13.11.2023; Ogledov: 531; Prenosov: 272
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9. Decision support tool for the management of dynamic genetic conservation unitsA. Rudow, Marjana Westergren, J. Buiteveld, Václav Buriánek, B. Cengel, Joan Cottrell, G. de Dato, K. Järve, Davorin Kajba, Colin Kelleher, François Lefèvre, M. Liesebach, L. Nagy, Srđan Stojnić, M. Villar, L. Yrjänä, Michele Bozzano, 2020, končno poročilo o rezultatih raziskav Ključne besede: decision support tool, genetic conservation
Objavljeno v DiRROS: 14.01.2021; Ogledov: 1335; Prenosov: 640
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10. Measuring techniques for concentration and stable isotopologues of CO2 in a terrestrial ecosystem : a reviewGrega E. Voglar, Saša Zavadlav, Tom Levanič, Mitja Ferlan, 2019, pregledni znanstveni članek Povzetek: Measurements of carbon dioxide and their stable isotopes are propulsive research tool in ecology and environmental science as they can give us insight into carbon cycle. They are widely used to investigate both natural and anthropogenic carbon sources in the atmosphere, hydrosphere and geosphere, as well as the exchange between these reservoirs. In this paper, we provide a basic overview of two different analytical measurement techniques, isotope ratio mass spectrometry (IRMS) and laser-absorption spectroscopy (LAS) which have been developed and utilized for monitoring of CO2 isotopologues in ecosystem. We present the basics for each technique, however with the emphasis on LAS measurement technique we are targeting readers who are not familiar with this topic. A major objective of this paper is to illustrate the current value and future potential of various analytical instruments in a wide range of applications deployed in the terrestrial ecosystem. Finally, we draw a conclusion from recent research campaigns by presenting a decision tree to better understand and choose a correct application combination for a selected scale of ecosystem.
Ključne besede: Isotope ratio mass spectrometry, laser-absorption spectroscopy, CO2 isotopologues, terrestrial ecosystem, decision tree, spectroscopic databases
Objavljeno v DiRROS: 18.02.2020; Ogledov: 1908; Prenosov: 904
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