1691. Long term response of electrochemotherapy with reduced dose of bleomycin in elderly patients with head and neck non-melanoma skin cancerČrt Jamšek, Gregor Serša, Maša Omerzel, Aleš Grošelj, 2020, original scientific article Abstract: . Electrochemotherapy (ECT) is a local cancer treatment based on electroporation where the electric field is used to enhance cell membrane permeability and thereby facilitating the transition of chemotherapeutic agents into the cell. For the treatment of non-melanoma skin cancer, a standard dosage of 15,000 IU/m2 bleomycin (BLM) is used. The aim of the present study was to evaluate the long-term ECT response in the group of elderly patients with non-melanoma skin cancer treated with a reduced dose of BLM in comparison to the outcome in the patients treated with the standard dose of BLM. Patients and methods. Twenty-eight patients older than 65 years, with a total of 52 non-melanoma skin lesions were included in the study. Twelve patients (24 lesions) in the experimental group received a reduced dose of BLM (10,000 IU/m2), 16 patients (28 lesions) were treated with a standard dose of BLM (15,000 IU/m2). Results. No statistically significant difference in tumor control was observed between both groups. In the experimental group, tumors recurred in 39.0% of treated lesions in a median follow-up time of 28 months. In the control group, the recurrence rate of treated lesions was 15.4% in a median follow-up time of 40 months. Conclusions. ECT with a reduced dose of BLM is a feasible treatment option for elderly patients with equal efficacy to standard dose treatment and should be considered as a treatment modality in advanced aged patients with comorbidities, where overall life expectancy is poor
Keywords: electrochemotherapy, bleomycin, non-melanoma skin cancer
Published in DiRROS: 12.07.2024; Views: 406; Downloads: 93
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1692. Tomato brown rugose fruit virus in aqueous environments : survival and significance of water-mediated transmissionNataša Mehle, Katarina Bačnik, Irena Bajde, Jakob Brodarič, Adrian Fox, Ion Gutiérrez-Aguirre, Miha Kitek, Denis Kutnjak, Yue Lin Loh, Olivera Maksimović, Maja Ravnikar, Elise Vogel, Christine Vos, Ana Vučurović, 2023, original scientific article Abstract: Tomato brown rugose fruit virus (ToBRFV) has recently emerged as a major disease of tomatoes and peppers. ToBRFV is a seed- and contact-transmitted virus. In Slovenia, ToBRFV RNA was detected in samples of wastewater, river, and water used to irrigate plants. Even though the source of detected RNA could not be clearly established, this raised the question of the significance of the detection of ToBRFV in water samples and experimental studies were performed to address this question. The data presented here confirm that the release of virus particles from the roots of infected plants is a source of infectious ToBRFV particles in water and that the virus can remain infective up to four weeks in water stored at room temperature, while its RNA can be detected for much longer. These data also indicate that irrigation with ToBRFV-contaminated water can lead to plant infection. In addition, it has been shown that ToBRFV circulated in drain water in commercial tomato greenhouses from other European countries and that an outbreak of ToBRFV can be detected by regular monitoring of drain water. A simple method for concentrating ToBRFV from water samples and a comparison of the sensitivity of different methods, including the determination of the highest ToBRFV dilution still capable of infecting test plants, were also investigated. The results of our studies fill the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the role of water-mediated transmission, and provide a reliable risk assessment to identify critical points for monitoring and control.
Keywords: tomato brown rugose fruit virus, tomato, hydroponics, water-linked epidemiology, survival
Published in DiRROS: 12.07.2024; Views: 379; Downloads: 308
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1693. Three-dimensional MRI evaluation of the effect of bladder volume on prostate translocation and distortionŽiga Snoj, Andrew B. Gill, Leonardo Rundo, Nikola Sushentsev, Tristan Barrett, 2020, original scientific article Keywords: prostate translocation, prostate distortion, gland deformation, bladder volume, magnetic resonance imaging, radiation therapy planning
Published in DiRROS: 12.07.2024; Views: 341; Downloads: 127
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1694. Pulsed low dose-rate irradiation response in isogenic HNSCC cell lines with different radiosensitivityVesna Todorović, Ajda Prevc, Martina Nikšić Žakelj, Monika Savarin, Simon Buček, Blaž Grošelj, Primož Strojan, Maja Čemažar, Gregor Serša, 2020, original scientific article Abstract: . Management of locoregionally recurrent head and neck squamous cell carcinomas (HNSCC) is challenging due to potential radioresistance. Pulsed low-dose rate (PLDR) irradiation exploits phenomena of increased radiosensitivity, low-dose hyperradiosensitivity (LDHRS), and inverse dose-rate effect. The purpose of this study was to evaluate LDHRS and the effect of PLDR irradiation in isogenic HNSCC cells with different radiosensitivity. Materials and methods. Cell survival after different irradiation regimens in isogenic parental FaDu and radioresistant FaDu-RR cells was determined by clonogenic assay; post irradiation cell cycle distribution was studied by flow cytometry; the expression of DNA damage signalling genes was assesed by reverse transcription-quantitative PCR. Results. Radioresistant Fadu-RR cells displayed LDHRS and were more sensitive to PLDR irradiation than parental FaDu cells. In both cell lines, cell cycle was arrested in G2/M phase 5 hours after irradiation. It was restored 24 hours after irradiation in parental, but not in the radioresistant cells, which were arrested in G1-phase. DNA damage signalling genes were under-expressed in radioresistant compared to parental cells. Irradiation increased DNA damage signalling gene expression in radioresistant cells, while in parental cells only few genes were under-expressed. Conclusions. We demonstrated LDHRS in isogenic radioresistant cells, but not in the parental cells. Survival of LDHRSpositive radioresistant cells after PLDR was significantly reduced. This reduction in cell survival is associated with variations in DNA damage signalling gene expression observed in response to PLDR most likely through different regulation of cell cycle checkpoints.
Keywords: DNA damage, isogenic cell lines, low dose irradiation, pulsed low dose-rate irradiation, radiosensitivity
Published in DiRROS: 12.07.2024; Views: 371; Downloads: 109
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1695. Looking beyond virus detection in RNA sequencing data : lessons learned from a community-based effort to detect cellular plant pathogens and pestsAnnelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Gaafar, Oscar Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovšek, Irena Mavrič Pleško, 2023, original scientific article Abstract: High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.
Keywords: plant viruses, plant virus detection, plant virology, high-throughput sequencing, RNA sequencing, plant tissues, plant pathogen, diagnostics, high-throughput sequencing, metagenomics, metatranscriptomics
Published in DiRROS: 12.07.2024; Views: 453; Downloads: 185
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1696. Leafhopper males compensate for unclear directional cues in vibration-mediated mate localizationJernej Polajnar, Ana Kuhelj, Rok Janža, Nada Žnidaršič, Tatjana Simčič, Meta Virant-Doberlet, 2023, original scientific article Abstract: Ambient noise and transmission properties of the substrate pose challenges in vibrational signal-mediated mating behavior of arthropods, because vibrational signal production is energetically demanding. We explored implications of these challenges in the leafhopper Aphrodes makarovi (Insecta: Hemiptera: Cicadellidae) by exposing males to various kinds of vibrational noise on a natural substrate and challenging them to find the source of the female playback. Contrary to expectations, males exposed to noise were at least as efficient as control males on account of similar searching success with less signaling effort, while playing back male–female duets allowed the males to switch to satellite behavior and locate the target without signaling, as expected. We found altered mitochondrial structure in males with high signaling effort that likely indicate early damaging processes at the cellular level in tymbal muscle, but no relation between biochemical markers of oxidative stress and signaling effort. Analysis of signal transmission revealed ambiguous amplitude gradients, which might explain relatively low searching success, but it also indicates the existence of behavioral adaptations to complex vibrational environments. We conclude that the observed searching tactic, emphasizing speed rather than thorough evaluation of directional cues, may compensate for unclear stimuli when the target is near.
Keywords: biotremology, vibrational communication, sexual behavior of insects, impact of noise on behavior, metabolism of vibrational production
Published in DiRROS: 12.07.2024; Views: 300; Downloads: 262
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1697. Increasing information content and diagnosability in family-level classificationsMatjaž Kuntner, Klemen Čandek, Matjaž Gregorič, Eva Turk, A. Chris Hamilton, Lisa Chamberland, James Starrett, Ren-Chung Cheng, Jonathan A. Coddington, Ingi Agnarsson, Jason E. Bond, 2023, original scientific article Abstract: Higher-level classifications often must account for monotypic taxa representing depauperate evolutionary lineages and lacking synapomorphies of their better-known, well-defined sister clades. In a ranked (Linnean) or unranked (phylogenetic) classification system, discovering such a depauperate taxon does not necessarily invalidate the rank classification of sister clades. Named higher taxa must be monophyletic to be phylogenetically valid. Ranked taxa above the species level should also maximize information content, diagnosability, and utility (e.g., in biodiversity conservation). In spider classification, families are the highest rank that is systematically catalogued, and incertae sedis is not allowed. Consequently, it is important that family level taxa be well defined and informative. We revisit the classification problem of Orbipurae, an unranked suprafamilial clade containing the spider families Nephilidae, Phonognathidae, and Araneidae sensu stricto. We argue that, to maximize diagnosability, information content, conservation utility, and practical taxonomic considerations, this “splitting” scheme is superior to its recently proposed alternative, which lumps these families together as Araneidae sensu lato. We propose to redefine Araneidae and recognize a monogeneric spider family, Paraplectanoididae fam. nov. to accommodate the depauperate lineage Paraplectanoides. We present new subgenomic data to stabilize Orbipurae topology which also supports our proposed family-level classification. Our example from spiders demonstrates why classifications must be able to accommodate depauperate evolutionary lineages, e.g., Paraplectanoides. Finally, although clade age should not be a criterion to determine rank, other things being equal, comparable ages of similarly ranked taxa do benefit comparative biology.
Keywords: classification, family rank, phylogenomics, systematics, monophyly, spider phylogeny, zoology
Published in DiRROS: 12.07.2024; Views: 382; Downloads: 267
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1698. Coastal fish fauna in the Cystoseira s.l. algal belts : experiences from the Northern Adriatic SeaLovrenc Lipej, Danijel Ivajnšič, Valentina Pitacco, Domen Trkov, Borut Mavrič, Martina Orlando-Bonaca, 2023, original scientific article Abstract: Cystoseira s.l. forests are recognised as important habitats which host diverse coastal fish assemblages. Many fish species use such habitats as feeding, breeding, and nursery grounds. Since the coastal fish community depends on the availability of dense macroalgal belts, the decline of these habitats in the Mediterranean Sea also affects the density of coastal fish species. We studied the coastal fish assemblage in Cystoseira s.l. forests in three consecutive years 2019–2021 in the Gulf of Trieste (Adriatic Sea). Data on coastal fish fauna were collected by visual counts conducted by SCUBA diving. Data on algal cover and habitat types were obtained by recording with a video camera. Similarities and differences in the fish community were analysed in terms of habitat and substrate preferences. A total of 34 species were recorded in Cystoseira forests. The results of the present study show that the different algal cover and associated depth gradient have different effects on the fish assemblage in coastal waters, affecting species composition and abundance. For many species, particularly labrids and sea breams, there is a decreasing temporal trend in frequency of occurrence and density. However, fish community trends can be used as a good “proxy” to evaluate the algal belt status. Our results indicate that rapid conservation and restoration actions are needed to stem the decline of Cystoseira s.l. forests.
Keywords: Cystoseira s.l. forests, fish assemblage, fish biodiversity, habitat preference, macroalgal belt, Mediterranean Sea
Published in DiRROS: 12.07.2024; Views: 349; Downloads: 213
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1699. New records of introduced species in the Mediterranean Sea (April 2023)Ana Fortič, Reem Al-Sheikh Rasheed, Zouhair Almajid, Ali Badreddine, José Carlos Báez, Ángel Belmonte-Gallegos, Nicola Bettoso, Diego Borme, Federica Camisa, Martina Orlando-Bonaca, 2023, original scientific article Abstract: This Collective article reports 17 introduced species and 22 new locations for these species in the Mediterranean Sea. The reports are from three different Marine Strategy Framework Directive (MSFD) subregions (Aegean-Levantine Sea, Adriatic Sea and Western Mediterranean Sea) and the Sea of Marmara and cover ten different countries. The goal of consistent and detailed reporting of introduced species is to complement the existing species inventories and serve as a basis for establishing monitoring strategies and other conservation measures. Some of the reports from this article are the first species records for the Mediterranean Sea, namely the green alga Udotea flabellum from the Aegean Sea (Turkey) and the deepbody boarfish Antigonia capros from the Balearic Sea (Spain). In addition, new records of introduced species are included for different seas, namely the moon crab Matuta victor for the Aegean Sea (Greece), the whale shark Rhincodon typus and the lionfish Pterois miles for the Alboran Sea (Spain), the almaco jack Seriola rivoliana for the Tyrrhenian Sea (Italy), and the hound needlefish Tylosurus crocodilus for the Adriatic Sea (Italy). Furthermore, reports on first country records are included: the red alga Colaconema codicola from Slovenia, the nudibranch Melibe viridis from Bosnia and Herzegovina, the lionfish Pterois miles from Montenegro, and the goldstripe sardinella Sardinella gibbosa from Syria, which also represents a second record for the Mediterranean Sea. Furthermore, the occurrence of the scleractinian coral Oculina patagonica was noted in Gulf of Lion (France). Four polychaete species, namely Leodice antennata, Timarete punctata and Branchiomma bairdi, are reported from the vermetid reef habitat and two of them (L. antennata and B. bairdi) are also recorded for the first time in Lebanon. Evidence for established populations of the Asian date mussel Arcuatula senhousia in the Sea of Marmara (Turkey) and the rayed pearl oyster Pinctada radiata around the island of Sardinia (Italy) is provided.
Published in DiRROS: 12.07.2024; Views: 445; Downloads: 450
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1700. Evaluation of DNA extraction methods for reliable quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosaAlexandra Bogožalec Košir, Dane Lužnik, Viktorija Tomič, Mojca Milavec, 2023, original scientific article Abstract: Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
Keywords: nucleic acid, dPCR, DNA extraction methods, Gram-negative bacteria
Published in DiRROS: 12.07.2024; Views: 413; Downloads: 296
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