1. Predator-prey interactions and eavesdropping in vibrational communication networksMeta Virant-Doberlet, Ana Kuhelj, Jernej Polajnar, Rok Šturm, 2019, review article Abstract: Due to human perceptional bias in favor of air-borne sounds, substrate-borne vibrational signaling has been traditionally regarded as a highly specialized, inherently short-range and, consequently, a private communication channel, free from eavesdropping by sexual competitors and predators. In this review, we synthesize current knowledge pertinent to the view that most animals live in a rich vibratory world, where vibrational information is available to unintended receivers. In recent years, we realized that vibrational signaling is one of the oldest and taxonomically most widespread forms of communication by mechanical waves and that receptors detecting substrate vibrations are ubiquitous. In nature, substrate vibrations are reliable source of information readily available to all members of the animal community able to detect them. Viewing vibrational communication in more relevant ecological context reveals that animals relying on substrate vibrations live in complex communication networks. Long evolutionary history of this communication channel is reflected in varied and sophisticated predator-prey interactions guided by substrate-borne vibrations. Eavesdropping and exploitation of vibrational signals used in sexual communication have been so far largely neglected; however, existing studies show that generalist arthropod predators can intercept such signals emitted by insects to obtain information about prey availability and use that information when making foraging decisions. Moreover, males which advertise themselves for longer periods than females and with vibrational signals of higher amplitude face higher predation risk. It is likely that eavesdropping and exploitation of vibrational signals are major drivers in the evolution taking place in the vibratory world and we believe that studies of interspecific interactions guided by substrate vibrations will, in the future, offer numerous opportunities to unravel mechanisms that are central to understanding behavior in general.
Keywords: biotremology, vibrational communication, communication network, predator-prey interactions, eavesdropping
Published in DiRROS: 06.08.2024; Views: 66; Downloads: 108
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2. Loop-mediated isothermal amplification of specific endoglucanase gene sequence for detection of the bacterial wilt pathogen Ralstonia solanacearumRok Lenarčič, Dany Morisset, Manca Pirc, Pablo Llop, Maja Ravnikar, Tanja Dreo, 2014, original scientific article Abstract: The increased globalization of crops production and processing industries also promotes the side-effects of more rapid and efficient spread of plant pathogens. To prevent the associated economic losses, and particularly those related to bacterial diseases where their management relies on removal of the infected material from production, simple, easy-to-perform, rapid and cost-effective tests are needed. Loop-mediated isothermal amplification (LAMP) assays that target 16S rRNA, fliC and egl genes were compared and evaluated as on-site applications. The assay with the best performance was that targeted to the egl gene, which shows high analytical specificity for diverse strains of the betaproteobacterium Ralstonia solanacearum, including its non-European and non-race 3 biovar 2 strains. The additional melting curve analysis provides confirmation of the test results. According to our extensive assessment, the egl LAMP assay requires minimum sample preparation (a few minutes of boiling) for the identification of pure cultures and ooze from symptomatic material, and it can also be used in a high-throughput format in the laboratory. This provides sensitive and reliable detection of R. solanacearum strains of different phylotypes.
Keywords: plant pathogens, bacterial diseases
Published in DiRROS: 02.08.2024; Views: 89; Downloads: 52
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3. Protein gas vesicles of bacillus megaterium as enhancers of ultrasound-induced transcriptional regulationVid Jazbec, Nina Varda, Ernest Šprager, Maja Meško, Sara Vidmar, Rok Romih, Marjetka Podobnik, Andreja Kežar, Roman Jerala, Mojca Benčina, 2024, original scientific article Published in DiRROS: 01.08.2024; Views: 126; Downloads: 162
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4. Rak neznanega izvora : nas izvor bolezni še zanimaErika Matos, Snežana Pavlović Djokić, Srdjan Novaković, Marina Čakš, Rok Devjak, Nežka Hribernik, Kaja Cankar, 2024, professional article Abstract: Rak neznanega izvora (RNI) je opredeljen kot karcinom ali nediferencirana neoplazma, pri kateri z naborom standardnih diagnostičnih postopkov ni mogoče odkriti izvornega mesta bolezni. Tradicionalno RNI delimo v dve podskupini, pri čemer le približno 15 % primerov predstavlja prognostično ugodno skupino. Velika večina bolnikov spada v prognostično neugodno skupino in ima ob prvi prezentaciji obsežno breme bolezni. Možnosti zdravljenja so omejene, izidi bolnikov, zdravljenih z empirično kemoterapijo (KT) s platino ali taksani, pa so še vedno slabi, srednje celokupno preživetje je manj kot 10 mesecev. Za mnoge bolnike ostaja optimalna izbira najboljše možno podporno zdravljenje. Novi pristopi k obravnavi teh bolnikov se zdijo obetavni in so temeljit premik v paradigmi zdravljenja RNI; od zdravljenja, specifičnega za organ/tkivo, k zdravljenju, usmerjenemu na posameznega bolnika, ki temelji na genomskih spremembah njegovega tumorja. Prispevek povzema trenutne dokaze o uporabi vsakega od teh pristopov. Predstavljeno je tudi zdravljenje treh bolnikov z neugodnim RNI.
Keywords: rak neznanega izvora, molekularne značilnosti, biološki označevalci
Published in DiRROS: 26.07.2024; Views: 138; Downloads: 89
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5. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevinePolona Kogovšek, Jennifer Hodgetts, J. Hall, Nina Prezelj, Petra Nikolić, Nataša Mehle, Rok Lenarčič, Ana Rotter, M. Dickinson, Neil Boonham, Marina Dermastia, Maja Ravnikar, 2015, original scientific article Abstract: In Europe the most devastating phytoplasma associated with grapevine yellows (GY) diseases is a quarantine pest, flavescence dorée (FDp), from the 16SrV taxonomic group. The on-site detection of FDp with an affordable device would contribute to faster and more efficient decisions on the control measures for FDp. Therefore, a real-time isothermal LAMP assay for detection of FDp was validated according to the EPPO standards and MIQE guidelines. The LAMP assay was shown to be specific and extremely sensitive, because it detected FDp in all leaf samples that were determined to be FDp infected using quantitative real-time PCR. The whole procedure of sample preparation and testing was designed and optimized for on-site detection and can be completed in one hour. The homogenization procedure of the grapevine samples (leaf vein, flower or berry) was optimized to allow direct testing of crude homogenates with the LAMP assay, without the need for DNA extraction, and was shown to be extremely sensitive.
Keywords: flavescence dorée, homogenization, loop-mediated isothermal amplification, on-site application, validation
Published in DiRROS: 26.07.2024; Views: 109; Downloads: 92
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6. Imaging microvascular changes in nonocular oncological clinical applications by optical coherence tomography angiography : a literature reviewRok Hren, Gregor Serša, Urban Simončič, Matija Milanič, 2023, review article Keywords: optical coherence tomography, angiography, endoscopy, oncology, skin carcinoma
Published in DiRROS: 26.07.2024; Views: 251; Downloads: 98
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7. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, Nina Gunde-Cimerman, Tine Grebenc, Cene Gostinčar, 2017, original scientific article Abstract: The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
Keywords: Deinococcus-Thermus, Deinococcaceae, Deinococcus ficus, radiation-resistant, rod-shaped, phenotype characterization, genome analysis, phylogenetic analysis
Published in DiRROS: 25.07.2024; Views: 118; Downloads: 96
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8. Cell proliferation on polyethylene terephthalate treated in plasma created in ▫$SO_2/O_2$▫ mixturesNina Recek, Matic Resnik, Rok Zaplotnik, Miran Mozetič, Helena Motaln, Tamara Lah Turnšek, Alenka Vesel, 2017, original scientific article Abstract: Samples of polymer polyethylene terephthalate were exposed to a weakly ionized gaseous plasma to modify the polymer surface properties for better cell cultivation. The gases used for treatment were sulfur dioxide and oxygen of various partial pressures. Plasma was created by an electrodeless radio frequency discharge at a total pressure of 60 Pa. X-ray photoelectron spectroscopy showed weak functionalization of the samples’ surfaces with the sulfur, with a concentration around 2.5 at %, whereas the oxygen concentration remained at the level of untreated samples, except when the gas mixture with oxygen concentration above 90% was used. Atomic force microscopy revealed highly altered morphology of plasma-treated samples; however, at high oxygen partial pressures this morphology vanished. The samples were then incubated with human umbilical vein endothelial cells. Biological tests to determine endothelialization and possible toxicity of the plasma-treated polyethylene terephthalate samples were performed. Cell metabolic activity (MTT) and in vitro toxic effects of unknown compounds (TOX) were assayed to determine the biocompatibility of the treated substrates. The biocompatibility demonstrated a well-pronounced maximum versus gas composition which correlated well with development of the surface morphology.
Published in DiRROS: 25.07.2024; Views: 82; Downloads: 85
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10. Safety and efficacy of drug-eluting microspheres chemoembolization under cone beam computed tomography control in patients with early and intermediate stage hepatocellular carcinomaŠpela Koršič, Nastja Levašič, Rok Dežman, Lara Anja Lešnik Zupan, Blaž Trotovšek, Rado Janša, Lojze Šmid, Peter Popović, 2022, original scientific article Abstract: Background. Drug-eluting microsphere transarterial chemoembolization (DEM-TACE) is the standard of care in pa-tients with intermediate-stage hepatocellular carcinoma and ensures targeted and controlled cytotoxic and ischemic effects. Proper patient selection and optimized treatment techniques are associated with longer median survival. The aim of this single-institution retrospective study was to evaluate safety and efficacy of DEM-TACE under cone beam computed tomography (CBCT) control in patients with early and intermediate stagehepatocellular carcinoma.Patients and methods. A total of144 patients (mean age 67.9 ± 8.0 years, 127 males and 17 females) between February 2010 and December 2018 were studied. Microparticles of different dimensions according to two manufac-turers (diameter of 70–150 μm, 100–300 μm or 300–500 μm and 40-μm, 75-μm or 100-μm) were used and loaded with 50–150 mg of doxorubicin. The objective tumour response according to the modified Response Evaluation Criteria in Solid Tumours (mRECIST), the time to progression, adverse events and overall survival were (OS) evaluated.Results. In total, 452 procedures were performed (median, 3 per patient). Four (0.9% of all procedures) major com-plications were noted. Postembolization syndrome occurred after 35% of procedures. At the first imaging follow-up 2–3 months after first treatment, 91% of patients achieved an objective response. The median time to progression was 10.2 months (95% CI: 8.3-12.1 months). OS rates at 1, 2, 3, 4, and 5 years were 85%, 53%, 33%, 20% and 14%, respectively. The median survival time was 25.8 months (95% CI: 22.1–29.5 months). Conclusions. DEM-TACE under CBCT control in patients with early and intermediate stagehepatocellular carcinoma is a safe and effective method of treatment with high objective tumour response and survival rates.
Keywords: hepatocellular carcinoma, drug-eluting microspheres, doxorubicin
Published in DiRROS: 25.07.2024; Views: 195; Downloads: 56
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