101. Extracellular vesicle-bound DNA in urine is indicative of kidney allograft injuryIvana Sedej, Maja Štalekar, Magda Tušek-Žnidarič, Katja Goričar, Nika Kojc, Polona Kogovšek, Vita Dolžan, Miha Arnol, Metka Lenassi, 2022, original scientific article Abstract: Extracellular vesicle-bound DNA (evDNA) is an understudied extracellular vesicle (EV) cargo, particularly in cancer-unrelated research. Although evDNA has been detected in urine, little is known about its characteristics, localization, and biomarker potential for kidney pathologies. To address this, we enriched EVs from urine of well-characterized kidney transplant recipients undergoing allograft biopsy, characterized their evDNA and its association to allograft injury. The SEC-based method enriched pure EVs from urine of kidney transplant recipients, regardless of the allograft injury. Urinary evDNA represented up to 29.2 ± 8% (mean ± SD) of cell-free DNA (cfDNA) and correlated with cfDNA in several characteristics but was less fragmented (P < 0.001). Importantly, using DNase treatment and immunogold labelling TEM, we demonstrated that evDNA was bound to the surface of urinary EVs. Normalised evDNA yield (P = 0.042) and evDNA copy number (P = 0.027) significantly differed between patients with normal histology, rejection injury and non-rejection injury, the later groups having significantly larger uEVs (mean diameter, P = 0.045) and more DNA bound per uEV. ddDNA is detectable in uEV samples of kidney allograft recipients, but its quantity is highly variable. In a proof-of-principle study, several evDNA characteristics correlated with clinical and histological parameters (P = 0.040), supporting that the potential of evDNA as a biomarker for kidney allograft injury should be further investigated.
Keywords: DNA, donor-derived DNA, extracellular vesicles
Published in DiRROS: 26.02.2025; Views: 105; Downloads: 76
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102. Inactivation of the Mla system and outer-membrane phospholipase A results in disrupted outer-membrane lipid asymmetry and hypervesiculation in Bordetella pertussisEline F. de Jonge, Lana Vogrinec, Ria van Boxtel, Jan Tommassen, 2022, original scientific article Abstract: Bordetella pertussis is the causative agent of a respiratory infection known as whooping cough. With the goal of improving the production of outer-membrane vesicles (OMVs), we studied here the mechanisms that are involved in maintaining lipid asymmetry in the outer membrane of this organism. We identified homologues of the phospholipid (PL)-transport systems Mla and Pqi and of outer-membrane phospholipase A (OMPLA). Inactivation of mlaF, encoding the ATPase of the Mla system, together with pldA, which encodes OMPLA, resulted in an accumulation of PLs at the cell surface as demonstrated by the binding of a phosphatidylethanolamine-specific fluorescent probe to intact cells of this strain. The corresponding single mutations did hardly or not affect binding of the probe. These results are consistent with a retrograde transport directionality of the Mla system in B. pertussis and indicate that PLs accumulating at the cell surface in the mlaF mutant are degraded by OMPLA. Consequently, the mlaF mutant showed a conditional growth defect due to the production of free fatty acids by OMPLA, which could be compensated by inactivation of OMPLA or by sequestration of the produced fatty acids with starch. The mlaF pldA double mutant showed markedly increased OMV production, and representative antigens were detected in these OMVs as in wild-type OMVs. Further phenotypic characterization showed that the barrier function of the outer membrane of the mlaF pldA mutant was compromised as manifested by increased susceptibility to SDS and to several antibiotics. Moreover, inactivation of mlaF alone or together with pldA resulted in increased biofilm formation, which was, however, not directly related to increased vesiculation as the addition of purified OMVs to the wild-type strain decreased biofilm formation. We conclude that the absence of MlaF together with OMPLA results in PL accumulation in the outer leaflet of the outer membrane, and the increased vesiculation of the mutant could be useful in the development of novel, OMV-based pertussis vaccines.
Keywords: Bordetella pertussis, phospholipid transport, outer-membrane vesicles, Mla system, Outer-membrane phospholipase A, biofilms
Published in DiRROS: 26.02.2025; Views: 94; Downloads: 56
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103. Economic costs of biological invasions in terrestrial ecosystems in RussiaNatalia I. Kirichenko, Phillip Joschka Haubrock, Ross N. Cuthbert, Evgeny Akulov, Elena Karimova, Yury Shneyder, Chunlong Liu, Elena Angulo, Christophe Diagne, Franck Courchamp, 2021, original scientific article Abstract: Terrestrial ecosystems, owing to the presence of key socio-economic sectors such as agriculture and forestry, may be particularly economically affected by biological invasions. The present study uses a subset of the recently developed database of global economic costs of biological invasions (InvaCost) to quantify the monetary costs of biological invasions in Russia, the largest country in the world that spans two continents. From 2007 up to 2019, invasions costed the Russian economy at least US$ 51.52 billion (RUB 1.38 trillion, n = 94 cost entries), with the vast majority of these costs based on predictions or extrapolations (US$ 50.86 billion; n = 87) and, therefore, not empirically observed. Most cost entries exhibited low geographic resolution, being split between European and Asian parts of Russia (US$ 44.17 billion; n = 72). Just US$ 7.35 billion (n = 22) was attributed to the European part solely and none to the Asian part. Invasion costs were documented for 72 species and particularly insects (37 species). The empirically-observed costs, summing up to US$ 660 million (n = 7), were reported only for four species: two insects Agrilus planipennis Fairmaire and Cydalima perspectalis (Walker) and two plants Ambrosia artemisiifolia L. and Heracleum sosnowskyi Manden. The vast majority of economic costs were related to resource damages and economic losses, with very little reported expenditures on managing invasions in terrestrial ecosystems. In turn, agriculture (US$ 37.42 billion; n = 68) and forestry (US$ 14.0 billion; n = 20) were the most impacted sectors. Overall, we report burgeoning economic costs of invasions in Russia and identify major knowledge gaps, for example, concerning specific habitat types (i.e. aquatic) and management expenditures, as well as for numerous known invasive taxa with no reported economic costs (i.e. vertebrates). Given this massive, largely underestimated economic burden of invasions in Russia, our work is a call for improved reporting of costs nationally and internationally.
Keywords: direct and indirect losses, insects, InvaCost, invasive species, pathogens, Russian Federation, weeds
Published in DiRROS: 26.02.2025; Views: 119; Downloads: 45
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104. A contribution to the Slovenian spider fauna – VŽan Kuralt, Neža Pajek Arambašić, Maja Ferle, Rok Kostanjšek, 2024, original scientific article Abstract: The present study discusses and reports on 29 spider species new to Slovenian fauna, specifically: Larinioides patagiatus, Cyrtarachne ixoides, Pritha nana, Marinarozelotes adriaticus, Micaria micans, Scotophaeus blackwalli, Zelotes similis, Agyneta orites, Donacochara speciosa, Lasiargus hirsutus, Trichoncus sordidus, Walckenaeria vigilax, Alopecosa taeniata, Pardosa oreophila, Pardosa sordidata, Pardosa paludicola, Pardosa sphagnicola, Xerolycosa miniata, Mimetus laevigatus, Philodromus laricium, Philodromus vagulus, Attulus rupicola, Marpissa radiata, Micrommata ligurina, Euryopis quinqueguttata, Parasteatoda tabulata, Phoroncidia paradoxa, Rhomphaea rostrata, and Robertus mediterraneus.
Keywords: Araneae, new records, spiders, Slovenia, endemics, Neozoa, Southern Alps
Published in DiRROS: 26.02.2025; Views: 79; Downloads: 56
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106. Biological invasion costs reveal insufficient proactive management worldwideRoss N. Cuthbert, Christophe Diagne, Emma J. Hudgins, Anna Turbelin, Danish A. Ahmed, Céline Albert, Thomas W. Bodey, Elizabeta Briski, Franz Essl, Phillip Joschka Haubrock, Natalia I. Kirichenko, 2022, original scientific article Abstract: The global increase in biological invasions is placing growing pressure on the management of ecological and economic systems. However, the effectiveness of current management expenditure is difficult to assess due to a lack of standardised measurement across spatial, taxonomic and temporal scales. Furthermore, there is no quantification of the spending difference between pre-invasion (e.g. prevention) and post-invasion (e.g. control) stages, although preventative measures are considered to be the most cost-effective. Here, we use a comprehensive database of invasive alien species economic costs (InvaCost) to synthesise and model the global management costs of biological invasions, in order to provide a better understanding of the stage at which these expenditures occur. Since 1960, reported management expenditures have totalled at least US$95.3 billion (in 2017 values), considering only highly reliable and actually observed costs — 12-times less than damage costs from invasions ($1130.6 billion). Pre-invasion management spending ($2.8 billion) was over 25-times lower than post-invasion expenditure ($72.7 billion). Management costs were heavily geographically skewed towards North America (54%) and Oceania (30%). The largest shares of expenditures were directed towards invasive alien invertebrates in terrestrial environments. Spending on invasive alien species management has grown by two orders of magnitude since 1960, reaching an estimated $4.2 billion per year globally (in 2017 values) in the 2010s, but remains 1–2 orders of magnitude lower than damages. National management spending increased with incurred damage costs, with management actions delayed on average by 11 years globally following damage reporting. These management delays on the global level have caused an additional invasion cost of approximately $1.2 trillion, compared to scenarios with immediate management. Our results indicate insufficient management — particularly pre-invasion — and urge better investment to prevent future invasions and to control established alien species. Recommendations to improve reported management cost comprehensiveness, resolution and terminology are also made.
Keywords: biosecurity, delayed control and eradication, global trendsInva, costInvasive alien species, socio-economic impacts
Published in DiRROS: 26.02.2025; Views: 102; Downloads: 52
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107. The advantages of flow cytometry in comparison to fluorometric measurement in algal toxicity testTina Eleršek, 2012, original scientific article Abstract: Fluorometric measurements in algal toxicity tests are very commonly used as surrogate parameters for algal biomass. Although, fluorometry is a powerful technique, we have demonstrated that it is not suitable for determination of toxic effects of chemicals, which alter the fluorescence spectra. We recommendthe flow cytometry as the best technique for detecting algal and/or cyanobacterial cell count and fluorescence per cell. Flow cytometry has many advantages: little volume of algal/cyanobacterial sample required, suitable also for little algal/cyanobacterial cells, distinction between live and dead cells. Furthermore, flow cytometry reveals the early changes in fluorescence spectra as a consequence of the specific chemicals presence or stress, even though the cell count is not yet affected (an early marker for ecotoxicology testing).
Keywords: algae, cyanobacteria, ecotoxicity test, fluorescence, flow cytometry
Published in DiRROS: 26.02.2025; Views: 99; Downloads: 83
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108. Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbariaNatalia I. Kirichenko, Evgeny V. Zakharov, Carlos Lopez-Vaamonde, 2022, original scientific article Abstract: The lime leaf-miner, Phyllonorycter issikii is an invasive micromoth with an unusually higher number of haplotypes in the invaded area (Europe, Western Siberia) compared to its putative native region (East Asia). The origin of the genetic diversity in the neocolonized region remains unclear. We surveyed over 15 thousand herbarium specimens of lime trees (Tilia spp.) collected across the Palearctic over a period of 252 years (1764–2016) looking for preserved larvae within the archival leaf mines. We found 203 herbarium specimens with leaf mines of Ph. issikii collected in East Asia, one of them dating back to 1830, i.e. 133 years before the description of the species. In contrast, only 22 herbarium specimens collected in the West Palearctic in the last three decades (1987–2015) carried leaf mines. DNA barcoding of archival specimens revealed 32 haplotypes out of which 23 were novel (not known from modern populations) and found exclusively in East Asia. Six haplotypes are shared between both native and invaded areas and only two were responsible for the recent invasion of the Western Palearctic. The remarkable number of newly discovered haplotypes in archival populations supports East Asia as the native region and the source area of invasion.
Keywords: ecology, entomology, genetics, next-generation sequencing, zoology, invasive species
Published in DiRROS: 26.02.2025; Views: 104; Downloads: 48
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109. Muscle gene electrotransfer is increased by the antioxidant tempol in miceBoštjan Markelc, Gregor Tevž, Maja Čemažar, Simona Kranjc Brezar, Jaka Lavrenčak, Bojana Žegura, Justin Teissié, Gregor Serša, 2012, original scientific article Abstract: Electropermeabilization (EP) is an effective method of gene transfer into different tissues. During EP, reactive oxygen species (ROS) are formed, which could affect transfection efficiency. The role of generated ROS and the role of antioxidants in electrotransfer in myoblasts in vitro and in Musculus tibialis cranialis in mice were, therefore, investigated. We demonstrate in the study that during EP of C2C12 myoblasts, ROS are generated on the surface of the cells, which do not induce long-term genomic DNA damage. Plasmid DNA for transfection (pEGFP-N1), which is present outside the cells during EP, neutralizes the generated ROS. The ROS generation is proportional to the amplitude of the electric pulses and can be scavenged by antioxidants, such as vitamin C or tempol. When antioxidants were used during gene electrotransfer, the transfection efficiency of C2C12 myoblasts was statistically significantly increased 1.6-fold with tempol. Also in vivo, the transfection efficiency of M. tibialis cranialis in mice was statistically significantly increased 1.4-fold by tempol. The study indicates that ROS are generated on cells during EP and can be scavenged by antioxidants. Specifically, tempol can be used to improve gene electrotransfer into the muscle and possibly also to other tissues.
Keywords: electropermeabilization, gene electrotransfer, muscle, tempol, reactive oxygen species
Published in DiRROS: 26.02.2025; Views: 110; Downloads: 62
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110. Modulation of the proteasome pathway by nano-curcumin and curcumin in retinal pigment epithelial cellsJ. Emanuel Ramos de Carvalho, Milan T. Verwoert, Ilse M.C. Vogels, Sabine Schipper-Krom, Cornelis J. F. van Noorden, Eric A. Reits, Ingeborg Klaassen, Reinier O. Schlingemann, 2018, original scientific article Abstract: Introduction: Curcumin has multiple biological effects including the modulation of protein homeostasis by the ubiquitin-proteasome system. The purpose of this study was to assess the in vitro cytotoxic and oxidative effects of nano-curcumin and standard curcumin and characterize their effects on proteasome regulation in retinal pigment epithelial (RPE) cells. Methods: Viability, cell cycle progression, and reactive oxygen species (ROS) production were determined after treatment with nano-curcumin or curcumin. Subsequently, the effects of nano-curcumin and curcumin on proteasome activity and the gene and protein expression of proteasome subunits PA28α, α7, β5, and β5i were assessed. Results: Nano-curcumin (5-100 μM) did not show significant cytotoxicity or anti-oxidative effects against H2O2-induced oxidative stress, whereas curcumin (≥10 μM) was cytotoxic and a potent inducer of ROS production. Both nano-curcumin and curcumin induced changes in proteasome-mediated proteolytic activity characterized by increased activity of the proteasome subunits β2 and β5i/β1 and reduced activity of β5/β1i. Likewise, nano-curcumin and curcumin affected mRNA and protein levels of household and immunoproteasome subunits. Conclusions: Nano-curcumin is less toxic to RPE cells and less prone to induce ROS production than curcumin. Both nano-curcumin and curcumin increase proteasome-mediated proteolytic activity. These results suggest that nano-curcumin may be regarded as a proteasome-modulating agent of limited cytotoxicity for RPE cells.
Keywords: curcumin, nano-curcumin, proteasome, retinal pigment epithelium
Published in DiRROS: 26.02.2025; Views: 106; Downloads: 54
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