1. Annual recurrence of prokaryotic climax communities in shallow waters of the North MediterraneanMauro Celussi, Vincenzo Manna, Elisa Banchi, Viviana Fonti, Matteo Bazzaro, Vesna Flander-Putrle, Katja Klun, Martina Kralj, Neža Orel, Tinkara Tinta, 2024, original scientific article Abstract: In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.
Keywords: marine microbial ecology, coastal seas, microbial community analyses, marine biology, marine ecology
Published in DiRROS: 17.05.2024; Views: 17; Downloads: 6
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2. Indicated domination gameBoštjan Brešar, Csilla Bujtás, Vesna Iršič, Douglas F. Rall, Zsolt Tuza, 2024, original scientific article Abstract: Motivated by the success of domination games and by a variation of the coloring game called the indicated coloring game, we introduce a version of domination games called the indicated domination game. It is played on an arbitrary graph $G$ by two players, Dominator and Staller, where Dominator wants to finish the game in as few rounds as possible while Staller wants just the opposite. In each round, Dominator indicates a vertex $u$ of $G$ that has not been dominated by previous selections of Staller, which, by the rules of the game, forces Staller to select a vertex in the closed neighborhood of $u$. The game is finished when all vertices of $G$ become dominated by the vertices selected by Staller. Assuming that both players are playing optimally according to their goals, the number of selected vertices during the game is the indicated domination number, $\gamma_{\rm i}(G)$, of $G$. We prove several bounds on the indicated domination number expressed in terms of other graph invariants. In particular, we find a place of the new graph invariant in the well-known domination chain, by showing that $\gamma_{\rm i}(G)\ge \Gamma(G)$ for all graphs $G$, and by showing that the indicated domination number is incomparable with the game domination number and also with the upper irredundance number. In connection with the trivial upper bound $\gamma_{\rm i}(G)\le n(G)-\delta(G)$, we characterize the class of graphs $G$ attaining the bound provided that $n(G)\ge 2\delta(G)+2$. We prove that in trees, split graphs and grids the indicated domination number equals the independence number. We also find a formula for the indicated domination number of powers of paths, from which we derive that there exist graphs in which the indicated domination number is arbitrarily larger than the upper irredundance number. We provide some partial results supporting the statement that $\gamma_{\rm i}(G)=n(G)/2$ if $G$ is a cubic bipartite graph, and leave this as an open question.
Keywords: domination game, indicated coloring, independence number, upper domination number
Published in DiRROS: 16.05.2024; Views: 36; Downloads: 14
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3. Ingenious architecture and coloration generation in enamel of Rodent teethVesna Šrot, Sophia Houari, Gregor Kapun, Birgit Bußmann, Felicitas Predel, Boštjan Pokorny, Elena Bužan, Ute Salzberger, Bernhard Fenk, Marion Kelsch, Peter van Aken, 2024, original scientific article Abstract: Teeth exemplify architectures comprising an interplay of inorganic and organic constituents, resulting in sophisticated natural composites. Rodents (Rodentia) showcase extraordinary adaptations, with their continuously growing incisors surpassing human teeth in functional and structural optimizations. In this study, employing state-of-the-art direct atomic-scale imaging and nanoscale spectroscopies, we present compelling evidence that the release of material from ameloblasts and the subsequent formation of iron-rich enamel and surface layers in the constantly growing incisors of rodents are complex orchestrated processes, intricately regulated and independent of environmental factors. The synergistic fusion of three-dimensional tomography and imaging techniques of etched rodent́s enamel unveils a direct correlation between the presence of pockets infused with ferrihydrite-like material and the acid resistant properties exhibited by the iron-rich enamel, fortifying it as an efficient protective shield. Moreover, observations using optical microscopy shed light on the role of iron-rich enamel as a microstructural element that acts as a path for color transmission, although the native color remains indistinguishable from that of regular enamel, challenging the prevailing paradigms. The redefinition of “pigmented enamel” to encompass ferrihydrite-like infusion in rodent incisors reshapes our perception of incisor microstructure and color generation. The functional significance of acid-resistant iron-rich enamel and the understanding of the underlying coloration mechanism in rodent incisors have far-reaching implications for human health, development of potentially groundbreaking dental materials, and restorative dentistry. These findings enable the creation of an entirely different class of dental biomaterials with enhanced properties, inspired by the ingenious designs found in nature.
Keywords: teeth microstructure, ameloblasts, ferritin, Fe-rich enamel, tomography, rodent
Published in DiRROS: 26.04.2024; Views: 66; Downloads: 70
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5. Adjuvant TNF-a therapy to electrochemotherapy with intravenous cisplatin in murine sarcoma exerts synergistic antitumor effectivenessMaja Čemažar, Vesna Todorović, Janez Ščančar, Urša Lampreht Tratar, Monika Savarin, Urška Kamenšek, Simona Kranjc Brezar, Andrej Cör, Gregor Serša, 2015, original scientific article Abstract: Background. Electrochemotherapy is a tumour ablation modality, based on electroporation of the cell membrane, allowing non-permeant anticancer drugs to enter the cell, thus augmenting their cytotoxicity by orders of magnitude. In preclinical studies, bleomycin and cisplatin proved to be the most suitable for clinical use. Intravenous administration of cisplatin for electrochemotherapy is still not widely accepted in the clinics, presumably due to its lower antitumor effectiveness, but adjuvant therapy by immunomodulatory or vascular-targeting agents could provide a way for its potentiation. Hence, the aim of the present study was to explore the possibility of adjuvant tumour necrosis factor % (TNF-%) therapy to potentiate antitumor effectiveness of electrochemotherapy with intravenous cisplatin administration in murine sarcoma. Materials and methods. In vivo study was designed to evaluate the effect of TNF-% applied before or after the electrochemotherapy and to evaluate the effect of adjuvant TNF-% on electrochemotherapy with different cisplatin doses. Results. A synergistic interaction between TNF-% and electrochemotherapy was observed. Administration of TNF-% before the electrochemotherapy resulted in longer tumour growth delay and increased tumour curability, and was significantly more effective than TNF-% administration after the electrochemotherapy. Tumour analysis revealed increased platinum content in tumours, TNF-% induced blood vessel damage and increased tumour necrosis after combination of TNF-% and electrochemotherapy, indicating an anti-vascular action of TNF-%. In addition, immunomodulatory effect might have contributed to curability rate of the tumours. Conclusion. Adjuvant intratumoural TNF-% therapy synergistically contributes to electrochemotherapy with intravenous cisplatin administration. Due to its potentiation at all doses of cisplatin, the combined treatment is predicted to be effective also in tumours, where the drug concentration is suboptimal or in bigger tumours, where electrochemotherapy with intravenous cisplatin is not expected to be sufficiently effective.
Keywords: electrochemotherapy, TNF, adjuvant immunotherapy, cisplatin
Published in DiRROS: 17.04.2024; Views: 122; Downloads: 27
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7. Domination and independence numbers of large 2-crossing-critical graphsVesna Iršič, Maruša Lekše, Miha Pačnik, Petra Podlogar, Martin Praček, 2023, original scientific article Abstract: After 2-crossing-critical graphs were characterized in 2016, their most general subfamily, large 3-connected 2-crossing-critical graphs, has attracted separate attention. This paper presents sharp upper and lower bounds for their domination and independence number.
Keywords: crossing-critical graphs, domination number, independence number
Published in DiRROS: 09.04.2024; Views: 84; Downloads: 51
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8. Generalized Pell graphsVesna Iršič, Sandi Klavžar, Elif Tan, 2023, original scientific article Abstract: In this paper, generalized Pell graphs $\Pi_{n,k}$, $k\ge 2$, are introduced. The special case of $k=2$ are the Pell graphs $\Pi_{n}$ defined earlier by Munarini. Several metric, enumerative, and structural properties of these graphs are established. The generating function of the number of edges of $\Pi_{n,k}$ and the generating function of its cube polynomial are determined. The center of $\Pi_{n,k}$ is explicitly described; if $k$ is even, then it induces the Fibonacci cube $\Gamma_{n}$. It is also shown that $\Pi_{n,k}$ is a median graph, and that $\Pi_{n,k}$ embeds into a Fibonacci cube.
Keywords: Fibonacci cubes, Pell graphs, generating functions, center of graph, median graphs, k-Fibonacci sequence
Published in DiRROS: 08.04.2024; Views: 116; Downloads: 46
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9. Long term follow-up report of cardiac toxicity in patients with multiple myeloma treated with tandem autologous hematopoietic stem cell transplantationMirta Koželj, Samo Zver, Vesna Zadnik, 2013, original scientific article Abstract: Background. Tandem autologous hematopoietic stem cell transplantation (ta-HSCT) is a standard treatment for multiple myeloma (MM). Patients receive a high-dose cyclophosphamide (CY), followed by two myeloablative cycles of melphalan (MEL). There are scarce data about long term cardiotoxicity. Patients and methods. We studied 12 patients (62.25 8.55 years) six years after the completion of MM treatment with ta-HCST. Late cardiotoxic effects were evaluated clinically and echocardiographically. Results. None of the patients developed clinical signs of heart failure, all were in sinus rhythm and NT-pro BNP concentration was elevated (778 902.76 pg/mL). The left ventricular (LV) size remained normal. The LV ejection fraction did not decrease (73.75 5.67%, 69.27 6.13%, p = NS). The LV diastolic function parameters (E, A, ratio E/A and A/a) did not change significantly. In tissue Doppler parameters we observed a nonsignificant decrease in Em (10.26 2.63 cm/s, 7.57 1.43 cm/s) and Sm velocities (8.7 0.87 cm/s, 7.14 1.17 cm/s, p = NS). The E/Em values were in an abnormal range (8.66 1.05, 10.55 2.03). Conclusions. The treatment of MM with ta-HSCT, during which patients receive a high dose CY followed by two myeloablative cycles of MEL, causes mild, chronic, partially reversible and clinically silent cardiotoxic side-effects. However, ta-HSCT in patients with MM is a safe regarding cardiotoxic side effects, but, because of increasing life expectancy needs long term attention.
Keywords: cardiotoxicity, echocardiography, myeloma
Published in DiRROS: 22.03.2024; Views: 131; Downloads: 36
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10. Assessment of the tumourigenic and metastatic properties of SK-MEL28 melanoma cells surviving electrochemotherapy with bleomycinVesna Todorović, Gregor Serša, Vid Mlakar, Damjan Glavač, Maja Čemažar, 2012, original scientific article Abstract: Background. Electrochemotherapy is a local treatment combining chemotherapy and electroporation and is highly effective treatment approach for subcutaneous tumours of various histologies. Contrary to surgery and radiation, the effect of electrochemotherapy on metastatic potential of tumour cells has not been extensively studied. The aim of the study was to evaluate the effect of electrochemotherapy with bleomycin on the metastatic potential of human melanoma cells in vitro. Materials and methods. Viable cells 48 hours after electrochemotherapy were tested for their ability to migrate and invade through Matrigel coated porous membrane. In addition, microarray analysis and quantitative Real-Time PCR were used to detect changes in gene expression after electrochemotherapy. Results. Cell migration and invasion were not changed in melanoma cells surviving electrochemotherapy.Interestingly, only a low number of tumourigenesis related genes was differentially expressed after electrochemotherapy. Conclusions. Our data suggest that metastatic potential of human melanoma cells is not affected by electrochemotherapy with bleomycin, confirming safe role of electrochemotherapy in the clinics.
Published in DiRROS: 21.03.2024; Views: 318; Downloads: 56
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