701. 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: 151; Downloads: 85
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702. 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: 137; Downloads: 98
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703. 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: 165; Downloads: 124
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704. 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: 126; Downloads: 71
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705. 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: 121; Downloads: 125
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706. 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: 594; Downloads: 169
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707. 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: 139; Downloads: 136
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708. Simple and reliable in situ CRISPR-Cas9 nuclease visualization tool is ensuring efficient editing in Streptomyces speciesAlen Pšeničnik, Roman Reberšek, Lucija Slemc, Tim Godec, Luka Kranjc, Hrvoje Petković, 2022, original scientific article Abstract: CRISPR-Cas9 technology has emerged as a promising tool for genetic engineering of Streptomyces strains. However, in practice, numerous technical hurdles have yet to be overcome when developing robust editing procedures. Here, we developed an extension of the CRISPR-Cas toolbox, a simple and reliable cas9 monitoring tool with transcriptional fusion of cas9 nuclease to a beta glucuronidase (gusA) visual reporter gene. The Cas9-SD-GusA tool enables in situ identification of cells expressing Cas9 nuclease following the introduction of the plasmid carrying the CRISPR-Cas9 machinery. Remarkably, when the Cas9-SD-GusA system was applied under optimal conditions, 100% of the colonies displaying GusA activity carried the target genotype. In contrast, it was shown that the cas9 sequence had undergone major recombination events in the colonies that did not exhibit GusA activity, giving rise to “escaper colonies” carrying unedited genotype. Our approach allows a simple detection of “escaper” phenotype and serves as an efficient CRISPR-Cas9 optimisation tool. Keywords: CRISPR-Cas9, gusA visual screening, "CRISPR escaper colonies", Streptomyces Published in DiRROS: 17.07.2024; Views: 134; Downloads: 123
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709. CRISPR/Cas9-mediated fine-tuning of miRNA expression in tetraploid potatoTjaša Lukan, Florian Veillet, Maja Križnik, Anna Coll Rius, Tjaša Mahkovec Povalej, Karmen Pogačar, Katja Stare, Laura Chauvin, Jean-Eric Chauvin, Kristina Gruden, 2022, original scientific article Abstract: MicroRNAs (miRNAs) are small noncoding RNAs, which modulate the abundance and spatiotemporal accumulation of target mRNAs at transcriptional and post-transcriptional levels and through that play important roles in several biological processes in plants. Here we show that in polyploid species, CRISPR/Cas9 system can be used for fine-tuning of miRNA expression, which can have broader range of applications compared to knock-out mutants. We established the complete pipeline for CRISPR-Cas9-mediated modulation of miRNA expression in potato. It consists of (1) design and assembly of dual sgRNA CRISPR/Cas9 constructs, (2) transient transfection of protoplasts following fast and efficient screening by high resolution melting analysis to select functional sgRNAs, and (3) stable transformation of potato explants with functional sgRNAs and selection of regenerated transgenic lines with desired mutations and desired miRNA abundance based on sequencing and RT-qPCR. We show that miRNA-editing using dual sgRNA approach results in different types of mutations among transgenic lines but also in different alleles of the same plant, which are target site-dependent. The most frequent were short deletions, but we also detected 1-nt insertions (T or G), deletions between two sgRNAs and larger deletions. miRNA abundance correlates with the frequency and type of introduced mutations, as more extensive mutations in more alleles result in lower miRNA abundance. Interestingly, some mutated loci can generate alternative miRNAs, now novel targets were however predicted for those. In all transgenic lines with Cas9 expression, we detected mutations, suggesting high efficiency of Cas9-editing. We confirmed the miRNA-editing efficiency of our optimised approach in two different potato genotypes and three different loci. Keywords: CRISPR/Cas9, hypersensitive response (HR)-conferred resistance, immune signaling, live cell imaging, Solanum tuberosum (potato), spatiotemporal analysis, stromules, virus resistance Published in DiRROS: 17.07.2024; Views: 143; Downloads: 144
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710. Quantitative assessment of the apical and basolateral membrane expression of VEGFR2 and NRP2 in VEGF-A-stimulated cultured human umbilical vein endothelial cellsEsmeralda K. Bosma, Shahan Darwesh, Jia Y. Zheng, Cornelis J. F. van Noorden, Reinier O. Schlingemann, Ingeborg Klaassen, 2022, original scientific article Abstract: Endothelial cells (ECs) form a precisely regulated polarized monolayer in capillary walls. Vascular endothelial growth factor-A (VEGF-A) induces endothelial hyperpermeability, and VEGF-A applied to the basolateral side, but not the apical side, has been shown to be a strong barrier disruptor in blood–retinal barrier ECs. We show here that VEGF-A presented to the basolateral side of human umbilical vein ECs (HUVECs) induces higher permeability than apical stimulation, which is similar to results obtained with bovine retinal ECs. We investigated with immunocytochemistry and confocal imaging the distribution of VEGF receptor-2 (VEGFR2) and neuropilin-2 (NRP2) in perinuclear apical and basolateral membrane domains. Orthogonal z-sections of cultured HUVECs were obtained, and the fluorescence intensity at the apical and basolateral membrane compartments was measured. We found that VEGFR2 and NRP2 are evenly distributed throughout perinuclear apical and basolateral membrane compartments in unstimulated HUVECs grown on Transwell inserts, whereas basolateral VEGF-A stimulation induces a shift toward basolateral VEGFR2 and NRP2 localization. When HUVECs were grown on coverslips, the distribution of VEGFR2 and NRP2 across the perinuclear apical and basolateral membrane domains was different. Our findings demonstrate that HUVECs dynamically regulate VEGFR2 and NRP2 localization on membrane microdomains, depending on growth conditions and the polarity of VEGF-A stimulation. Keywords: endotelijske celice, EGF, celična biologija Published in DiRROS: 17.07.2024; Views: 127; Downloads: 119
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