621. The depleted carbon isotopic signature of nematodes and harpacticoids and their place in carbon processing in fish farm sedimentsMateja Grego, Alenka Malej, Marleen De Troch, 2020, izvirni znanstveni članek Povzetek: Fish farm-originating organic matter can modify the ecological processes in a benthic ecosystem. This was investigated in the sediments of the northern Adriatic Sea by measuring δ13C signature of nematodes, harpacticoids, and sedimentary organic matter, and by assessing pore water nutrients and bacterial composition. In a mesocosm experiment, 13C-labeled diatoms were added on top of sediment cores and 13C enrichment was measured as a proxy of diatom uptake by meiofauna. The δ13C signatures were depleted under fish farming cages compared to the reference site, as observed for sedimentary organic matter (−24.4‰ vs. −21.8‰), for nematodes (−22.5‰ vs. −17.7‰), and for harpacticoids (−25.3‰ vs. −20.8‰). The direct consumption of fish feed (−22.2‰) was not traced in meiofauna taxa. Nematodes from the farm site likely reflect a diet comprising sedimentary organic matter, as they were enriched by 2‰ relative to the sedimentary organic matter. The nematodes from the reference site were enriched by 4.2‰ relative to the sedimentary organic matter, which implies that they rely on more enriched food sources, like diatoms, which was confirmed by their uptake of 13C-labeled diatoms. The nematode assemblage incorporated more diatom 13C than harpacticoids, making them more important players in the carbon flux from diatoms to higher trophic levels at the reference site. Harpacticoids from the reference site were enriched by 1.1‰ compared to sedimentary organic matter, implying that this was their primary food source. Harpacticoids from the farm site were depleted by 0.9‰ relative to the sedimentary organic matter, indicating they were influenced by a very depleted food source like bacteria. Harpacticoids from both the cage and reference sites consumed 13C-labeled diatoms, which implies their diet might span a broad δ13C range, from bacteria to diatoms. Pore water nutrients with high dissolved inorganic carbon, phosphate, and ammonium concentration indicated an elevated microbial degradation of organic compounds under the fish farm. The denaturing gradient gel electrophoresis analysis showed a 70% similarity between sediment bacteria communities from the fish farm and reference site. The study demonstrated that fish farm-originating organic matter enters the meiofauna food chain, and that nematodes and harpacticoids use different food sources under the fish farm and at the reference site. Objavljeno v DiRROS: 22.07.2024; Ogledov: 142; Prenosov: 115
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622. Supporting dataset and methods for body sizes and concentrations of chemical elements measured in elytra and abdomens of Stag Beetles Lucanus cervusGrzegorz Orłowski, Lucyna Mróz, Marcin Kadej, Adrian Smolis, Dariusz Tarnawski, Jerzy Karg, Alessandro Campanaro, Marco Bardiani, Deborah J. Harvey, Marcos Méndez, Arno Thomaes, Al Vrezec, Krzysztof Ziomek, Andrzej L. Rudecki, Detlef Mader, 2020, izvirni znanstveni članek Povzetek: The dataset presented in this data paper supports “Breaking down insect stoichiometry into chitin-based and internal elemental traits: Patterns and correlates of continent-wide intraspecific variation in the largest European saproxylic beetle” (Orłowski et al. 2020). Here we present the supplementary data and description of methods on the following: (1) mass of elytra and abdomens across 28 local Stag Beetle Lucanus cervus populations in Europe. (2) Population origin and coverage of six major land-cover types, including transport infrastructure, measured in three radii (500 m, 1000 m and 5000 m) around the sampling sites of these populations. (3) The relationship between the mass and concentrations of elements measured in abdomens and elytra in 28 Stag Beetle populations and major land-cover types around the sampling sites. Ključne besede: elemental composition, trace elements, internal metal concentrations, exoskeleton, chitin-bound metals Objavljeno v DiRROS: 22.07.2024; Ogledov: 156; Prenosov: 97
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623. Evidence for senescence in survival but not in reproduction in a short-lived passerineRémi Fay, Michael Schaub, Jennifer A. Border, Ian G. Henderson, Georg Fahl, Jürgen Feulner, Petra Horch, Mathis Müller, Helmut Rebstock, Dmitry Shitikov, Davorin Tome, Matthias Vögeli, Martin U. Grüebler, 2020, izvirni znanstveni članek Povzetek: Senescence has been studied since a long time by theoreticians in ecology and evolution, but empirical support in natural population has only recently been accumulating. One of the current challenges is the investigation of senescence of multiple fitness components and the study of differences between sexes. Until now, studies have been more frequently conducted on females than on males and rather in long-lived than in short-lived species. To reach a more fundamental understanding of the evolution of senescence, it is critical to investigate age-specific survival and reproduction performance in both sexes and in a large range of species with contrasting life histories. In this study, we present results on patterns of age-specific and sex-specific variation in survival and reproduction in the whinchat Saxicola rubetra, a short-lived passerine. We compiled individual-based long-term datasets from seven populations that were jointly analyzed within a Bayesian modeling framework. We found evidence for senescence in survival with a continuous decline after the age of 1 year, but no evidence of reproductive senescence. Furthermore, we found no clear evidence for sex effects on these patterns. We discuss these results in light of previous studies documenting senescence in short-lived birds. We note that most of them have been conducted in populations breeding in nest boxes, and we question the potential effect of the nest boxes on the shape of age-reproductive trajectories. Ključne besede: actuarial senescence, age-specific demographic rate, aging, Saxicola rubetra, whinchat Objavljeno v DiRROS: 22.07.2024; Ogledov: 146; Prenosov: 98
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624. Transmission modes affect the population structure of potato virus Y in potatoWashington da Silva, Denis Kutnjak, Yi Xu, Yimin Xu, James Giovannoni, Santiago F. Elena, Stewart Gray, 2020, izvirni znanstveni članek Povzetek: Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution. Objavljeno v DiRROS: 22.07.2024; Ogledov: 141; Prenosov: 148
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625. CCR5-mediated signaling is involved in invasion of glioblastoma cells in its microenvironmentMetka Novak, Miha Koprivnikar Krajnc, Barbara Hrastar, Barbara Breznik, Bernarda Majc, Mateja Mlinar, Ana Rotter, Andrej Porčnik, Jernej Mlakar, Katja Stare, Richard G. Pestell, Tamara Lah Turnšek, 2020, izvirni znanstveni članek Povzetek: Abstract
The chemokine CCL5/RANTES is a versatile inflammatory mediator, which interacts with the receptor CCR5, promoting cancer cell interactions within the tumor microenvironment. Glioblastoma is a highly invasive tumor, in which CCL5 expression correlates with shorter patient survival. Using immunohistochemistry, we identified CCL5 and CCR5 in a series of glioblastoma samples and cells, including glioblastoma stem cells. CCL5 and CCR5 gene expression were significantly higher in a cohort of 38 glioblastoma samples, compared to low-grade glioma and non-cancerous tissues. The in vitro invasion of patients-derived primary glioblastoma cells and glioblastoma stem cells was dependent on CCL5-induced CCR5 signaling and is strongly inhibited by the small molecule CCR5 antagonist maraviroc. Invasion of these cells, which was enhanced when co-cultured with mesenchymal stem cells (MSCs), was inhibited by maraviroc, suggesting that MSCs release CCR5 ligands. In support of this model, we detected CCL5 and CCR5 in MSC monocultures and glioblastoma-associated MSC in tissue sections. We also found CCR5 expressing macrophages were in close proximity to glioblastoma cells. In conclusion, autocrine and paracrine cross-talk in glioblastoma and, in particular, glioblastoma stem cells with its stromal microenvironment, involves CCR5 and CCL5, contributing to glioblastoma invasion, suggesting the CCL5/CCR5 axis as a potential therapeutic target that can be targeted with repositioned drug maraviroc. Ključne besede: CCL5, CCR5, chemokines, glioblastoma, invasion, maraviroc, mesenchymal stem cells Objavljeno v DiRROS: 22.07.2024; Ogledov: 164; Prenosov: 35
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626. New records of rare species in the Mediterranean Sea (May 2020)Vasilis Gerovasileiou, Okan Akyol, Zinah Al-Hosne, Reem Alshikh Rasheed, Eylül Ataç, Giambattista Bello, Ilija Ćetković, Maria Corsini-Foka, Fabio Crocetta, Francesco Denitto, Paolo Guidetti, Benal Gül, Gianni Insacco, Lovrenc Lipej, Domen Trkov, 2020, izvirni znanstveni članek Povzetek: This Collective Article presents information about 17 taxa belonging to four Phyla (one Cnidaria, two Arthropoda, four Mollusca, and ten Chordata) and extending from the Western Mediterranean to the Levantine Sea. The new records were reported from nine countries as follows: Algeria: first published records of the clingfishes Apletodon dentatus and Lepadogaster lepadogaster after 1955; France: first record of the tripletail Lobotes surinamensis in French Mediterranean waters; Italy: new records of the rare bonito Orcynopsis unicolor and the recently described nudibranch Elysia rubeni from Sicily; first records of the parasitic cirriped Sacculina eriphiae and the nudibranch Dondice trainitoi in the Ionian Sea; first record of the nudibranch Taringa tritorquis in the Mediterranean Sea; first record of the tripletail Lobotes surinamensis in the North Ionian Sea; first documented record of the cephalopod Macrotritopus defilippi in the Adriatic Sea; Slovenia: first record of the Mediterranean endemic cryptobenthic goby Odondebuenia balearica; Montenegro: several recent occurrences of the critically endangered bull ray Aetomylaeus bovinus in the South-eastern Adriatic Sea; Greece: records of the nudibranch Dondice trainitoi in the Eastern Mediterranean Sea; new record of the occurrence of the Mediterranean spearfish Tetrapturus belone from Greece (Rhodes Island); Turkey: recent captures of the vulnerable ocean sunfish Mola mola, caught by purse-seine, in the Aegean Sea and the Dardanelles; new record of the luvar Luvarus imperialis along the Aegean coast of Turkey; Cyprus: first record of the habitat-forming hydroid Lytocarpia myriophyllum, often in considerable densities; first confirmed record of the agujon needlefish Tylosurus imperialis; Syria: first record of the decapod Ethusa mascarone. Objavljeno v DiRROS: 22.07.2024; Ogledov: 146; Prenosov: 106
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627. A new network for the advancement of marine biotechnology in Europe and beyondAna Rotter, Ariola Bacu, Michèle Barbier, Francesco Bertoni, Atle M. Bones, M. Leonor Cancela, Jens Carlsson, Maria F. Carvalho, Marta Cegłowska, Meltem Conk Dalay, Jerica Sabotič, 2020, izvirni znanstveni članek Povzetek: Marine organisms produce a vast diversity of metabolites with biological activities useful for humans, e.g., cytotoxic, antioxidant, anti-microbial, insecticidal, herbicidal, anticancer, pro-osteogenic and pro-regenerative, analgesic, anti-inflammatory, anti-coagulant, cholesterol-lowering, nutritional, photoprotective, horticultural or other beneficial properties. These metabolites could help satisfy the increasing demand for alternative sources of nutraceuticals, pharmaceuticals, cosmeceuticals, food, feed, and novel bio-based products. In addition, marine biomass itself can serve as the source material for the production of various bulk commodities (e.g., biofuels, bioplastics, biomaterials). The sustainable exploitation of marine bio-resources and the development of biomolecules and polymers are also known as the growing field of marine biotechnology. Up to now, over 35,000 natural products have been characterized from marine organisms, but many more are yet to be uncovered, as the vast diversity of biota in the marine systems remains largely unexplored. Since marine biotechnology is still in its infancy, there is a need to create effective, operational, inclusive, sustainable, transnational and transdisciplinary networks with a serious and ambitious commitment for knowledge transfer, training provision, dissemination of best practices and identification of the emerging technological trends through science communication activities. A collaborative (net)work is today compelling to provide innovative solutions and products that can be commercialized to contribute to the circular bioeconomy. This perspective article highlights the importance of establishing such collaborative frameworks using the example of Ocean4Biotech, an Action within the European Cooperation in Science and Technology (COST) that connects all and any stakeholders with an interest in marine biotechnology in Europe and beyond. Ključne besede: marine biotechnology, marine natural products, blue growth, marine biodiversity and chemodiversity, responsible research and innovation, stakeholder engagement, science communication, sustainability Objavljeno v DiRROS: 22.07.2024; Ogledov: 161; Prenosov: 87
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628. Digital PCR method for detection and quantification of specific antimicrobial drug-resistance mutations in human cytomegalovirusAlexandra Bogožalec Košir, Tašja Cvelbar, Martin Kammel, Hans-Peter Grunert, Heinz Zeichhardt, Mojca Milavec, 2020, izvirni znanstveni članek Povzetek: Antimicrobial drug resistance is one of the biggest threats to human health worldwide. Timely detection and quantification of infectious agents and their susceptibility to antimicrobial drugs are crucial for efficient management of resistance to antiviral drugs. In clinical settings, viral drug resistance is most often associated with prolonged treatment of chronic infections, and assessed by genotyping methods; e.g., sequencing and PCR. These approaches have limitations: sequencing can be expensive and does not provide quantification; and qPCR quantification is hampered by a lack of reference materials for standard curves. In recent years, digital PCR has been introduced, which provides absolute quantification without the need for reference materials for standard curves. Using digital PCR, we have developed a rapid, sensitive and accurate method for genotyping and quantification of the most prevalent mutations that cause human cytomegalovirus resistance to ganciclovir. Ključne besede: digital PCR, antimicrobial-drug resistance, HCMV, polymerase chain reaction, viruses Objavljeno v DiRROS: 22.07.2024; Ogledov: 163; Prenosov: 130
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629. European policies and legislation targeting ocean acidification in european waters : current stateCharles Galdies, Richard Bellerby, Donata Melaku Canu, Wenting Chen, Alenka Malej, 2020, izvirni znanstveni članek Povzetek: Ocean acidification (OA) is a global problem with profoundly negative environmental, social and economic consequences. From a governance perspective, there is a need to ensure a coordinated effort to directly address it. This study reviews 90 legislative documents from 17 countries from the European Economic Area (EEA) and the UK that primarily border the sea. The primary finding from this study is that the European national policies and legislation addressing OA is at best uncoordinated. Although OA is acknowledged at the higher levels of governance, its status as an environmental challenge is greatly diluted at the European Union Member State level. As a notable exception within the EEA, Norway seems to have a proactive approach towards legislative frameworks and research aimed towards further understanding OA. On the other hand, there was a complete lack of, or inadequate reporting in the Marine Strategy Framework Directive by the majority of the EU Member States, with the exception of Italy and the Netherlands. We argue that the problems associated with OA and the solutions needed to address it are unique and cannot be bundled together with traditional climate change responses and measures. Therefore, European OA-related policy and legislation must reflect this and tailor their actions to mitigate OA to safeguard marine ecosystems and societies. A stronger and more coordinated approach is needed to build environmental, economic and social resilience of the observed and anticipated changes to the coastal marine systems. Objavljeno v DiRROS: 22.07.2024; Ogledov: 139; Prenosov: 93
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630. Functional imaging of the ocular fundus using an 8-band retinal multispectral imaging systemJ. Emanuel Ramos de Carvalho, Richelle J. M. Hoveling, Cornelis J. F. van Noorden, Reinier O. Schlingemann, Maurice C. G. Aalders, 2020, izvirni znanstveni članek Povzetek: Application of functional imaging in ophthalmology requires efficient imaging techniques that can detect and quantify chromophores to visualise processes in vivo. The aim of the present study was to develop and evaluate a fast and affordable imaging system. We describe an eight-band retinal multispectral imaging (MSI) system and compare it with a hyperspectral imaging (HSI) device. Determination of blood oxygen saturation was studied as proof of principle. Reflectance of incident light is measured as 1/absorbance at different wavelengths between 440 nm and 580 nm. Both devices have incorporated optical bandpass filters in a mydriatic fundus camera. The MSI system scans the retina at eight pre-defined wavelengths specific for the spectrum of haemoglobin. The HSI system acquires a full scan from 480 to 720 nm in 5 nm steps. A simple assessment of the ratio between the absorbance peaks of oxygenated haemoglobin (HbO2) and reduced haemoglobin (HbR) was not suitable for generating validated oxygenation maps of the retina. However, a correction algorithm that compares the measured reflectance with reflectance spectra of fully oxygenated and fully deoxygenated blood allowed our MSI setup to estimate relative oxygen saturation at higher levels, but underestimated relative oxygen saturation at lower levels. The MSI device generated better quality images than the HSI device. It allows customisation with filter sets optimised for other chromophores of interest, and augmented with extrinsic contrast imaging agents, it has the potential for a wider range of ophthalmic molecular imaging applications. Ključne besede: functional imaging, multispectral imaging, hyperspectral imaging, oximetry Objavljeno v DiRROS: 22.07.2024; Ogledov: 453; Prenosov: 283
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