701. Trace metals and polycyclic aromatic hydrocarbons in the Eastern Mediterranean sediments : concentration ranges as a tool for quality control of large data collectionsMarina Lipizer, Branko Čermelj, 2022, original scientific article Abstract: Assessing the status of marine pollution at regional and sub-regional scales requires the use of comparable and harmonized data provided by multiple institutions, located in several countries. Standardized data management and quality control are crucial for supporting a coherent evaluation of marine pollution. Taking the Eastern Mediterranean Sea as a case study, we propose an approach to improve the quality control procedures used for sediment pollution data, thus supporting a harmonized environmental assessment. The regional ranges of contaminant concentrations in sediments were identified based on an in-depth literature review, and the lowest measured concentrations were evaluated to determine the “background concentrations” of chemical substances not yet targeted in the Mediterranean Sea. In addition, to verify the suitability of the approach for validating large data collections provided by multiple sources, the determined ranges were used to validate a regional dataset available through EMODnet data infrastructure. Published in DiRROS: 17.07.2024; Views: 136; Downloads: 97
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702. Soil water dynamics and olive yield (Olea europaea L.) under different surface drip irrigation treatments in northern MediterraneanMatic Noč, Urša Pečan, Marina Pintar, Maja Podgornik, 2024, original scientific article Abstract: The use of modern irrigation systems and monitoring of soil water status can help improve crop performance and water use efficiency. The influence of different irrigation treatments on soil water content dynamics and olive oil yield was studied over two growing seasons using a surface drip irrigation system in an olive grove in northern Mediterranean climate. Irrigation treatments included optimal irrigation, sustained deficit irrigation (33 % of optimal irrigation), and rainfed treatment. Based on the water applied, we calculated the percentage of replenished estimated evapotranspiration (ETc*) for each treatment using the Penman-Monteith method. Soil water content dynamics were monitored with capacitive probes at five depths (10 to 50 cm). The increase in soil water content at a depth of 30 to 50 cm, which was only achieved with optimal irrigation, resulted in a significantly higher olive oil yield. In contrast, deficit irrigation, despite the addition of water, did not lead to an increase in soil water in the layers below 30 cm, so that the yield was equal to that of rainfed treatment. In irrigated olive groves, it is beneficial to monitor the water content of the soil at several depths to ensure that a sufficient amount of water has been applied.Uporaba sodobnih namakalnih sistemov ter spremljanje stanja vode v tleh lahko pripomore k izboljšanju učinkovitosti rastlinske pridelave in rabe vode. Vpliv različnih načinov namakanja na dinamiko vsebnosti vode v tleh in pri-delek oljčnega olja smo preučevali v dveh rastnih dobah z upo-rabo površinskega kapljičnega namakalnega sistema v oljčnem nasadu v severnem sredozemskem podnebju. Obravnavanja so vključevala optimalno namakanje, trajno namakanje s priman-jkljajem (33 % optimalnega namakanja) in brez namakanja. Na podlagi porabljene vode smo z uporabo metode Penman-Mon-teith izračunali odstotek nadomeščene ocenjene evapotranspi-racije (ETc*) za vsako obravnavo. Dinamiko vsebnosti vode v tleh smo spremljali s kapacitivnimi merilniki na petih globinah (od 10 do 50 cm). Povečanje vsebnosti vode v tleh na globini od 30 do 50 cm, ki je bilo doseženo le z optimalnim namakanjem, je povzročilo večji pridelek oljčnega olja. Nasprotno pa se pri namakanju s primanjkljajem kljub dodajanju vode ni povečala količina vode v tleh v plasteh pod 30 cm, zato je bil pridelek enak pridelku brez namakanja. V namakanih oljčnih nasadih je koristno spremljati vsebnost vode v tleh na več globinah, da se zagotovi, da je bila priskrbljena zadostna količina vode Keywords: diviner, evapotranspiration, irrigation management, olive, soil depths, volumetric soil water content Published in DiRROS: 17.07.2024; Views: 135; Downloads: 161
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703. Learning deep representations of enzyme thermal adaptationGang Li, Filip Buric, Jan Zrimec, Sandra Viknander, Jens Nielsen, Aleksej Zelezniak, Martin K. M. Engqvist, 2022, original scientific article Abstract: Temperature is a fundamental environmental factor that shapes the evolution of organisms. Learning thermal determinants of protein sequences in evolution thus has profound significance for basic biology, drug discovery, and protein engineering. Here, we use a data set of over 3 million BRENDA enzymes labeled with optimal growth temperatures (OGTs) of their source organisms to train a deep neural network model (DeepET). The protein-temperature representations learned by DeepET provide a temperature-related statistical summary of protein sequences and capture structural properties that affect thermal stability. For prediction of enzyme optimal catalytic temperatures and protein melting temperatures via a transfer learning approach, our DeepET model outperforms classical regression models trained on rationally designed features and other deep-learning-based representations. DeepET thus holds promise for understanding enzyme thermal adaptation and guiding the engineering of thermostable enzymes. Keywords: bioinformatics, deep neural networks, enzyme catalytic temperatures, optimal growth temperatures, protein thermostability, transfer learning Published in DiRROS: 17.07.2024; Views: 169; Downloads: 137
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704. Optimization of a calcium-based treatment method for jellyfish to design food for the futureFrancesca Anna Ramires, Stefania De Domenico, Danilo Migoni, Francesco Paolo Fanizzi, Dror Angel, Rasa Slizyte, Katja Klun, Gianluca Bleve, Antonella Leone, 2022, original scientific article Abstract: Edible jellyfish are a traditional Southeast Asian food, usually prepared as a rehydrated product using a salt and alum mixture, whereas they are uncommon in Western Countries and considered as a novel food in Europe. Here, a recently developed, new approach for jellyfish processing and stabilization with calcium salt brining was upgraded by modifying the pre-treatment step of freshly caught jellyfish and successfully applied to several edible species. Treated jellyfish obtained by the application of the optimized version of this method respected both quality and safety parameters set by EU law, including no pathogenic microorganisms, absence or negligible levels of histamine and of total volatile basic nitrogen, no heavy metals; and the total bacterial, yeast, and mold counts were either negligible or undetectable. Jellyfish treated by the presented method exhibited unique protein content, amino acid and fatty acid profiles, antioxidant activity, and texture. The optimized method, initially set up on Rhiszostoma pulmo, was also successfully applied to other edible jellyfish species (such as Cotylorhiza tuberculata, Phyllorhiza punctata, and Rhopilema nomadica) present in the Mediterranean Sea. This study discloses an innovative process for the preparation of jellyfish-based food products for potential future distribution in Europe. Keywords: jellyfish, novel food, safety, quality, nutritional traits, organic calcium salts Published in DiRROS: 17.07.2024; Views: 157; Downloads: 95
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705. Long-term ringing data on migrating passerines reveal overall avian decline in EuropeTina Petras, Al Vrezec, 2022, original scientific article Abstract: The loss of biodiversity is shaping today’s environment. Bird ringing is a citizen science research tool that can determine species population dynamics and trends over a large geographic area. We used a 17-year time series to assess population trends of 74 passerine species based on ringing data from autumn migration in Slovenia (south-central Europe). We defined seven guilds of species according to geographic location, ecological, migratory, breeding, and life-history traits. Almost all guilds showed declining trends, except for the group of species of northeastern European origin, which showed a stable trend. The greatest decline was in low-productivity wetland specialists. Forest birds, seed-eaters, and high-productivity species experienced the smallest declines. The general declines in avifauna across a range of life-history and behavioural traits, and across a range of spatial and ecological scales, suggest widespread environmental change in Europe. Our data indicates that recent trends are toward ecosystem homogeneity, with an impoverished avifauna, including a few species that are increasing in abundance. These are the species with higher productivity and flexible behaviour, such as short-distance migrants, that have the greatest chance of prevailing in the recently rapidly changing environment because of their ability to adapt to changes in a timely manner. Keywords: bird population trends, ecological traits, life-history traits, migratory traits, recovery analysis, avifaunal change Published in DiRROS: 17.07.2024; Views: 156; Downloads: 114
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706. Transcriptional deregulation of stress-growth balance in Nicotiana benthamiana biofactories producing insect sex pheromonesMojca Juteršek, Marko Petek, Živa Ramšak, Elena Moreno Gimenéz, Silvia Gianoglio, Rubèn Mateos Fernández, Diego Orzaez, Kristina Gruden, Špela Baebler, 2022, original scientific article Abstract: Plant biofactories are a promising platform for sustainable production of high-value compounds, among which are insect sex pheromones, a green alternative to conventional insecticides in agriculture. Recently, we have constructed transgenic Nicotiana benthamiana plants (“Sexy Plants”, SxP) that successfully produce a blend of moth (Lepidoptera) sex pheromone compounds (Z)-11-hexadecen-1-ol and (Z)-11-hexadecenyl acetate. However, efficient biosynthesis of sex pheromones resulted in growth and developmental penalty, diminishing the potential for commercial use of SxP in biomanufacturing. To gain insight into the underlying molecular responses, we analysed the whole-genome transcriptome and evaluated it in relation to growth and pheromone production in low- and high-producing transgenic plants of v1.0 and v1.2 SxP lines. In our study, high-producing SxPv1.2 plants accumulated the highest amounts of pheromones but still maintained better growth compared to v1.0 high producers. For an in-depth biological interpretation of the transcriptomic data, we have prepared a comprehensive functional N. benthamiana genome annotation as well as gene translations to Arabidopsis thaliana, enabling functional information transfer by using Arabidopsis knowledge networks. Differential gene expression analysis, contrasting pheromone producers to wild-type plants, revealed that while only a few genes were differentially regulated in low-producing plants, high-producing plants exhibited vast transcriptional reprogramming. They showed signs of stress-like response, manifested as downregulation of photosynthesis-related genes and significant differences in expression of hormonal signalling and secondary metabolism-related genes, the latter presumably leading to previously reported volatilome changes. Further network analyses confirmed stress-like response with activation of jasmonic acid and downregulation of gibberellic acid signalling, illuminating the possibility that the observed growth penalty was not solely a consequence of a higher metabolic burden imposed upon constitutive expression of a heterologous biosynthetic pathway, but rather the result of signalling pathway perturbation. Our work presents an example of comprehensive transcriptomic analyses of disadvantageous stress signalling in N. benthamiana biofactory that could be applied to other bioproduction systems. Keywords: transcriptomics, plant biotechnology, jasmonic acid, growthstress tradeoffs, network analysis, growth penalty, insect sex pheromone Published in DiRROS: 17.07.2024; Views: 174; Downloads: 132
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707. An annotated checklist and the conservation status of Chondrichthyans in the AdriaticAlen Soldo, Lovrenc Lipej, 2022, original scientific article Abstract: Although there is a high number of publications listing fish species in the Adriatic, only a few have focused on chondrichthyans, while their conservation status has been investigated even less. Thus, this paper aims to provide an updated and annotated checklist of the chondrichthyans occurring in the Adriatic waters with their presence and conservation status. Each species is evaluated against the criteria defined in IUCN (International Union for Conservation of Nature) Red List Categories and Criteria and according to the guidelines for national and regional level assessments. In total, 60 chondrichthyan species from 27 families and 42 genera are listed. The list contains 33 species of sharks, 26 species of rays and one chimera. Assessment of the conservation status reveals that three species are now considered Regionally Extinct (namely Squatina oculata, Pristis pectinata and Rhinobatos rhinobatos). A total of 21 species are assessed as Critically Endangered, 8 are Endangered and 10 are Vulnerable. Of the remaining species, six are Near Threatened and the same number of species are Least Concern and Data Deficient. Considering that the principal driver of chondrichthyan decline and regional extinction is overfishing, it is recommended that the Adriatic countries adopt the same management measures and strengthen their coordination. Keywords: checklist, Chondrichthyans, Adriatic, conservation status, zoology, marine biology Published in DiRROS: 17.07.2024; Views: 137; Downloads: 75
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708. Observing and modeling long-term persistence of P. noctiluca in coupled complementary marine systems (Southern Tyrrhenian Sea and Messina Strait)Andrea Bergamasco, Andrea Cucco, Letterio Guglielmo, R. Minutoli, G. Quattrocchi, R. Guglielmo, Franca Palumbo, Marco Pansera, Giacomo Zagami, Martin Vodopivec, Alenka Malej, A. Granata, 2022, original scientific article Abstract: In the Mediterranean Sea, the Strait of Messina (MS) is a very peculiar area, connecting highly different regions and representing a privileged observatory for an early comprehension and assessment of ecosystems shifts. It is hypothesized that the outbreaks observed near the coast of many sites in the Mediterranean Sea may be the result of transport of permanent populations of P. noctiluca in pelagic waters to the coast, caused by specific hydrodynamic conditions. By both visual observations and numerical experiments our objective is twofold: (A) to help clarify whether the basin of the Aeolian Islands Archipelago (AIA), in the Southern Tyrrhenian Sea (STS), may be the site from which large populations of P. noctiluca are transported to the MS, and (B) to evaluate whether the upwelling turbulent system of the MS can be an energetic opportunity for this species. It should offer a rich habitat without jeopardizing the overall survival of the population, that is subject to stranding due to strong currents. Although very different, the two involved ecosystems (AIA and MS ) are complementary for the success of Pelagia noctiluca life cycle. Outputs obtained by coupling the 3D hydrodynamic model (SHYFEM) with a Lagrangian particle tracking model support the hypothesis of a connectivity between these two ecosystems, particularly in the first half of the year, indicating the coastal areas around the AIA as potential optimal source location for Pelagia larval stages. We support the very attractive hypothesis that two connected systems exist, the former one favours Pelagia's reproduction and acts as a nursery and the latter favours its growth due to higher productivity. We speculate that the reproductive population of the AIA is not permanent, but is renewed every year by individuals who have fed and quickly grown in the MS and who are passively transported by downwelling along canyon "corridors". Keywords: coastal systems, coastal water, Tyrrhenian Sea Published in DiRROS: 17.07.2024; Views: 129; Downloads: 131
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709. Biodiversity offset mechanisms and compensation for loss from exceptional to popular : rediscovering environmental lawJerneja Penca, 2024, original scientific article Abstract: The use of compensatory mechanisms for biodiversity conservation, also known as biodiversity offsets, has increased significantly in recent decades. The Kunming Montreal Global Biodiversity Framework mentions them as an innovative scheme in support of substantially and progressively increasing the level of financial resources for biodiversity conservation. This article traces the origin of compensatory mechanisms in international environmental law and their development in transnational biodiversity governance. The article points to the shifts in the application of the biodiversity offsets: from the context of wetlands to other habitats and ecosystems; from its use in intergovernmental conventions to an increasing number of transnational (business) networks; and from an instrument of last resort to a source of additional funding for biodiversity conservation. In the evolution, compensatory mechanisms have been decoupled from their original purpose as an exceptional mitigation measure and a strong focus of environmental law on the preventive function. The increased rhetoric of commitment to no net loss, net gain, restoration, and the mitigation hierarchy has not been matched by an improved status of wetlands and other ecosystems. The processes within the biodiversity conventions (Ramsar and CBD) have accepted an ongoing destruction of nature and limited the role of environmental law to minimizing harmful impacts on nature and consolidating the decline, rather than shaping socio-ecological outcomes. An ambiguous position about the spread of compensatory mechanisms has been part and parcel of this; biodiversity conventions have neither endorsed nor distanced themselves from the application, promotion, and justification of compensatory mechanisms. To maintain the integrity of environmental law, the rules that prevent biodiversity loss need to be emphasised and enforced. Keywords: biodiversity offsets, compensatory mechanisms, biodiversity governance, environmental law, preventive principles Published in DiRROS: 17.07.2024; Views: 597; Downloads: 177
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710. New alien Mediterranean biodiversity records (August 2022)Francesco Tiralongo, Okan Akyol, Sara A. A. Al-Mabruk, Pietro Battaglia, Damla Beton, Banu Bitls, John Joseph Borg, Marc Bouchoucha, Melih Ertan Çinar, Fabio Crocetta, Branko Dragičević, Jakov Dulčić, Athanasios Evangelopoulos, Julian Evans, Ana Fortič, Robin P. M. Gauff, Constantinos Georgiadis, Mehmet Gökoğlu, Daniele Grech, Tamar Guy-Haim, Mehmet Fatih Huseyinoglu, Domen Trkov, 2022, original scientific article Abstract: In this Collective Article on alien and cryptogenic diversity in the Mediterranean Sea we report a total of 19 species belonging to nine Phyla and coming from nine countries. Several of these records concern fish species, and of particular interest are the first records of: Terapon puta for Italian waters; Pteragopus trispilus from Malta; Plotosus lineatus from Cyprus; and the northernmost Mediterranean record of Lagocephalus sceleratus. The northernmost Mediterranean record was also reported for the sea urchin Diadema setosum. The portunid crab Thalamita poissonii was recorded for the first time in Libya. The copepod Pseudodiaptomus marinus was recorded for the first time in the Marmara Sea. The polychaete Branchiomma luctuosum was recorded for the first time from the Mediterranean coast of France. The alien anemone Diadumene lineata was recorded for the first time from Slovenia. The macroalgae Sargassum furcatum was recorded for the first time from Italy. The new Mediterranean records here reported help tracing abundance and distribution of alien and cryptic species in the Mediterranean Sea. Keywords: alien diversity, cryptogenic diversity, new species, Mediterranean Sea Published in DiRROS: 17.07.2024; Views: 150; Downloads: 145
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