611. 2D and 3D in vitro assays to quantify the invasive behavior of glioblastoma stem cells in response to SDF-1[alpha]Vashendriya V. V. Hira, Barbara Breznik, Cornelis J. F. van Noorden, Tamara Lah Turnšek, Remco J. Molenaar, 2020, original scientific article Abstract: Invasion is a hallmark of cancer and therefore in vitro invasion assays are important tools in cancer research. We aimed to describe in vitro 2D transwell assays and 3D spheroid assays to quantitatively determine the invasive behavior of glioblastoma stem cells in response to the chemoattractant SDF-1α. Matrigel was used as a matrix in both assays. We demonstrated quantitatively that SDF-1α increased invasive behavior of glioblastoma stem cells in both assays. We conclude that the 2D transwell invasion assay is easy to perform, fast and less complex whereas the more time-consuming 3D spheroid invasion assay is physiologically closer to the in vivo situation. Keywords: 2D transwell invasion assay, 3D spheroid invasion assay, cancer cell, cellular invasion, glioblastoma stem cells Published in DiRROS: 22.07.2024; Views: 133; Downloads: 125
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612. The effect of three polyphenols and some other anti-oxidant substances on amyloid fibril formation by human cystatin CAlma Jahić, Magda Tušek-Žnidarič, Sara Pintar, Selma Berbić, Eva Žerovnik, 2020, original scientific article Abstract: Human cystatin C (CysC) is an amyloid forming protein involved in the hereditary cerebral amyloid angiopathy (HCCAA) that affects arteries in the brain and the peripheral nervous system. In this study we measured the influence of several substances on human CysC aggregation and amyloid fibril formation, induced at pH 4 in vitro. The effect of three polyphenols: resveratrol, quercetin and curcumin and of two antioxidants: vitamin C (VitC) and N-acetyl-L-cysteine (NAC) was explored as well as the effect of sulphoraphane (SF) and α-lipoic acid (AL). The formation of amyloid fibrils was followed by Thioflavin T (ThT) fluorescence and by transmission electron microscopy (TEM). Effects on the length of the lag phase were revealed by following the increase of ThT fluorescence intensity with time. The amount and morphology of fibrils in comparison to prefibrillar aggregates and globular oligomers were evaluated by TEM at the plateau stage of the reaction. Thermal stabilization of the CysC monomer by the small compounds was measured by differential scanning fluorimetry (DSF). NAC, VitC and SF exhibited the largest inhibitory effect on amyloid fibril growth. The effects of polyphenols were not significant, apart from resveratrol, which partly inhibited the amyloid fibril growth. Published in DiRROS: 22.07.2024; Views: 130; Downloads: 85
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613. Validating the potential of double-stranded RNA targeting Colorado potato beetle mesh gene in laboratory and field trialsMarko Petek, Anna Coll Rius, Rok Ferenc, Jaka Razinger, Kristina Gruden, 2020, original scientific article Abstract: Colorado potato beetle (CPB) is an agricultural pest of solanaceous crops, notorious for its rapid resistance development to chemical pesticides. Foliar spraying of dsRNA formulations is a promising innovative technology providing highly specific and environmentally acceptable option for CPB management. We designed dsRNA to silence CPB mesh gene (dsMESH) and performed laboratory feeding trials to assess impacts on beetle survival and development. We compared the effectiveness of in vivo and in vitro produced dsRNA in a series of laboratory experiments. We additionally performed a field trial in which the efficacy of dsRNA sprayed onto potato foliage was compared to a spinosad-based insecticide. We showed that dsMESH ingestion consistently and significantly impaired larval growth and decreased larval survival in laboratory feeding experiments. In vivo produced dsRNA performed similarly as in vitro synthesized dsRNA in laboratory settings. In the field trial, dsMESH was as effective in controlling CPB larvae as a commercial spinosad insecticide, its activity was however slower. We discuss limitations and benefits of a potential dsMESH-based CPB management strategy and list some important RNAi based CPB research topics, which will have to be addressed in future. Keywords: RNA interference, RNA interference feeding, ds RNA, gene silencing, RNAi pest control, survival analysis, field trial Published in DiRROS: 22.07.2024; Views: 137; Downloads: 53
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614. Development and validation of a new TaqMan real-time PCR for detection of 'Candidatus phytoplasma pruni'Zala Kogej Zwitter, Marina Dermastia, Nataša Mehle, 2020, original scientific article Abstract: Phytoplasmas of the 16SrIII group are wide spread, and have a broad plant host range. Among these, ‘Candidatus phytoplasma pruni’ (‘Ca. P. pruni’; phytoplasmas of 16SrIII subgroup A) can cause serious diseases in Prunus species and ‘Ca. P. pruni’-related strains can infect other plant species, including grapevines. In this study, a new real-time PCR detection system was developed for ‘Ca. P. pruni’ using TaqMan chemistry. This test was designed to detect ‘Ca. P. pruni’, by amplifying the species-specific secY gene. In addition, a test to amplify the group-specific 16S rRNA gene region was also developed. The performances of both tests were evaluated. The test that amplifies the secY gene provided reliable and quick detection of ‘Ca. P. pruni’. Using the newly developed and validated test, ‘Ca. P. pruni’ was not found in any of the 434 field samples collected from different plants species grown in different regions of Slovenia. Keywords: phytoplasma, X-disease, real-time PCR, Prunus Published in DiRROS: 22.07.2024; Views: 144; Downloads: 145
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615. 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, original scientific article Abstract: 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. Published in DiRROS: 22.07.2024; Views: 117; Downloads: 104
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616. 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, original scientific article Abstract: 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. Keywords: elemental composition, trace elements, internal metal concentrations, exoskeleton, chitin-bound metals Published in DiRROS: 22.07.2024; Views: 124; Downloads: 82
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617. 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, original scientific article Abstract: 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. Keywords: actuarial senescence, age-specific demographic rate, aging, Saxicola rubetra, whinchat Published in DiRROS: 22.07.2024; Views: 131; Downloads: 82
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618. 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, original scientific article Abstract: 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. Published in DiRROS: 22.07.2024; Views: 125; Downloads: 134
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619. 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, original scientific article Abstract: 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. Keywords: CCL5, CCR5, chemokines, glioblastoma, invasion, maraviroc, mesenchymal stem cells Published in DiRROS: 22.07.2024; Views: 139; Downloads: 31
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620. 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, original scientific article Abstract: 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. Published in DiRROS: 22.07.2024; Views: 133; Downloads: 99
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