11. Stress tolerance of three opportunistic black yeastsJanja Zajc, Cene Gostinčar, Metka Lenassi, Nina Gunde-Cimerman, 2018, izvirni znanstveni članek Povzetek: Many species of black yeasts can survive extremely harsh conditions and can quickly adapt to novel environments. These traits were proposed to have a role in the ability of some fungal species tocolonise indoor habitats inhospitable for majority of microorganisms, and to cause (opportunistic)infections in humans. In order to better understand the stress tolerance of black yeasts and thereby their opportunism, we focused our research on the three model black yeasts: the polyextremotolerant Au-reobasidium melanogenum and Exophiala dermatitidis, and the extremely halotolerant Hortaeawerneckii. These black yeasts are shown to thrive at temperatures, salinities, pH values and, H2O2 concentrations that inhibit growth of mesophilic species. Most importantly, unlike their close relatives they can not only grow, but also synthesize siderophores (E. dermatitidis) or degradeproteins (A. melanogenum) at 37 °C - traits that are crucial for pathogenesis in humans. These results support the hypothesis that the ability to cope with various environmental stresses is linked to the opportunistic behaviour of fungi. Therefore, better understanding of the connections between the stress-tolerant biology of black fungi and their ability to cause disease is needed, in particular due to their changing interactions with humans and their emerging pathogenicity.
Ključne besede: melanised fungi, temperature, NaCl, pH tolerance, ROS, oligotrophism, proteolytic activity, capsule
Objavljeno v DiRROS: 01.08.2024; Ogledov: 225; Prenosov: 129
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12. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: flavescence dorée, homogenization, loop-mediated isothermal amplification, on-site application, validation
Objavljeno v DiRROS: 26.07.2024; Ogledov: 245; Prenosov: 216
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13. Transmembrane protein CD9 is glioblastoma biomarker, relevant for maintenance of glioblastoma stem cellsNeža Podergajs, Helena Motaln, Uroš Rajčević, Urška Verbovšek, Marjan Koršič, Nina Obad, Heidi Espedal, Miloš Vittori, Christel Herold-Mende, Hrvoje Miletic, Rolf Bjerkvig, Tamara Lah Turnšek, 2016, izvirni znanstveni članek Povzetek: The cancer stem cell model suggests that glioblastomas contain a subpopulation of stem-like tumor cells that reproduce themselves to sustain tumor growth. Targeting these cells thus represents a novel treatment strategy and therefore more specific markers that characterize glioblastoma stem cells need to be identified. In the present study, we performed transcriptomic analysis of glioblastoma tissues compared to normal brain tissues revealing sensible up-regulation of CD9 gene. CD9 encodes the transmembrane protein tetraspanin which is involved in tumor cell invasion, apoptosis and resistance to chemotherapy. Using the public REMBRANDT database for brain tumors, we confirmed the prognostic value of CD9, whereby a more than two fold up-regulation correlates with shorter patient survival. We validated CD9 gene and protein expression showing selective up-regulation in glioblastoma stem cells isolated from primary biopsies and in primary organotypic glioblastoma spheroids as well as in U87-MG and U373 glioblastoma cell lines. In contrast, no or low CD9 gene expression was observed in normal human astrocytes, normal brain tissue and neural stem cells. CD9 silencing in three CD133+ glioblastoma cell lines (NCH644, NCH421k and NCH660h) led to decreased cell proliferation, survival, invasion, and self-renewal ability, and altered expression of the stem-cell markers CD133, nestin and SOX2. Moreover, CD9-silenced glioblastoma stem cells showed altered activation patterns of the Akt, MapK and Stat3 signaling transducers. Orthotopic xenotransplantation of CD9-silenced glioblastoma stem cells into nude rats promoted prolonged survival. Therefore, CD9 should be further evaluated as a target for glioblastoma treatment.
Ključne besede: biomarker, CD9, glioblastoma stem cells, neural stem cells, tetraspanin
Objavljeno v DiRROS: 26.07.2024; Ogledov: 216; Prenosov: 149
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14. Metabolic consequences of infection of grapevine (Vitis vinifera L.) cv. ʺModra frankinjaʺ with flavescence dorée phytoplasmaNina Prezelj, Elizabeth Covington, Thomas Roitsch, Kristina Gruden, Lena Fragner, Wolfram Weckwerth, Marko Chersicola, Maja Vodopivec, Marina Dermastia, 2016, izvirni znanstveni članek Povzetek: Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp–grapevine interaction in infected grapevines of cv. “Modra frankinja” under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defense response status.
Ključne besede: fructose utilization, gene expression, invertase, metabolome, soluble sugars, starch, sucrose synthase, SWEET, VvDMR6
Objavljeno v DiRROS: 25.07.2024; Ogledov: 248; Prenosov: 217
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15. Modern approach to the management of genitourinary syndrome in women with gynecological malignanciesNina Kovačević, Ines Cilenšek, Sebastjan Merlo, Barbara Šegedin, 2023, pregledni znanstveni članek Povzetek: The term genitourinary syndrome of menopause was first used in 2014 by the North American Menopause Society and the International Society for the Study of Women's Sexual Health to describe conditions previously known as atrophic vaginitis, urogenital atrophy, or vulvovaginal atrophy. It is a complex, chronic, progressive condition characterized by a wide range of signs and symptoms affecting sexual function and the tissues of the urinary and genital tracts. The main cause of genitourinary syndrome of menopause is estrogen deficiency caused by ovarian removal or dysfunction. The most bothersome symptoms are vaginal dryness, decreased vaginal lubrication, and pain during penetration and intercourse. They all have a negative impact on the quality of life. Conclusions: The main goal of treatment is to relieve the symptoms. Treatment modalities are pharmacological or non-pharmacological. The first-line treatment for mild to moderate symptoms is the use of personal lubricants and moisturizers, but the gold standard is estrogen replacement therapy. Hormone therapy may not be an option for women with hormone-dependent cancer.
Ključne besede: genitourinary syndrome, gynecological malignancies, therapy
Objavljeno v DiRROS: 25.07.2024; Ogledov: 178; Prenosov: 56
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16. Does concurrent gynaecological surgery affect infectious complications rate after mastectomy with implant-based reconstruction?Nina Pišlar, Barbara Perić, Uroš Ahčan, Romi Cencelj-Arnež, Janez Žgajnar, Andraž Perhavec, 2023, izvirni znanstveni članek Povzetek: Background. Women who undergo breast cancer surgery often have an indication for gynaecological procedure. The aim of our study was to compare infectious complications rate after mastectomy with implant-based reconstruc-tion in patients with and without concurrent gynaecological procedure.Patients and methods. We retrospectively reviewed clinical records of 159 consecutively operated patients after mastectomy with implant-based reconstruction. The patients were divided in 2 groups: 102 patients without (Group 1) and 57 with (Group 2) concurrent gynaecological procedure. Infectious complications rates between the groups were compared using χ2-test. Logistic regression was performed to test for association of different variables with infec-tious complications.Results. There were240 breast reconstructions performed. Median follow-up time was 297 days (10–1061 days). Mean patient age was 47.2 years (95% CI 32.8–65.9); 48.2 years (95% CI 46.1–50.3) in Group 1 and 45.8 years (95% CI 43.2–48.3) in Group 2; p = 0.002). Infectious complications rate was 17.6% (17.6% vs. 17.5%, p = 0.987), implant loss occurred in 5.7% (4.9% vs. 7.0%, p = 0.58). Obesity (body mass index[BMI] > 30 kg/m2), age, previous breast conserv-ing treatment (BCT) with radiotherapy (RT) were identified as risk factors for infectious complications in univariate analysis. Obesity (adjusted odds ratio [aOR] 3.319, 95% CI 1.085–10.157, p = 0.036) and BCT with RT (aOR 7.481, 95% CI 2.230–25.101, p = 0.001) were independently associated with infectious complications in multivariate model.Conclusions. Concurrent gynaecological procedure for patients undergoing mastectomy with implant-based re-construction did not carry an increased risk for infectious complications.
Ključne besede: rak na dojki, infekcijski zapleti, rekonstrukcija z vsadki
Objavljeno v DiRROS: 25.07.2024; Ogledov: 203; Prenosov: 113
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17. Oral verrucous carcinoma : a diagnostic and therapeutic challengeNejc Krištofelc, Nina Zidar, Primož Strojan, 2023, pregledni znanstveni članek Povzetek: Background. Verrucous carcinoma is a low-grade variant of squamous cell carcinoma with specific morphologic, cytokinetic and clinical features. Despite low mitotic activity and slow growth, it can infiltrate adjacent tissues in advanced stages but does not metastasize. The most frequently affected site is the oral cavity. The following article provides latest updates in the etiology, clinical presentation, diagnostics and treatment options in oral verrucous car-cinoma and discusses the existing dilemmas linked to this unique malignancy.Conclusions. Oral verrucous carcinoma must be differentiated from conventional squamous cell carcinoma due to its less aggressive behaviour with a more favourable prognosis. Close communication between clinician and patholo-gist is mandatory for making a correct diagnosis. Primary surgery with negative surgical margins seems to be the most successful treatment. However, management recommendations are not uniform since they are mostly based on case reports and small retrospective case series. Prospective and pooled multi-institutional studies are therefore needed.
Ključne besede: verrucous carcinoma, oral verrucous carcinoma, squamous cell carcinoma
Objavljeno v DiRROS: 25.07.2024; Ogledov: 203; Prenosov: 178
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18. Treatment of vulvar cancer recurrences with electrochemotherapy : a detailed analysis of possible causes for unsuccessful treatmentGregor Vivod, Tanja Jesenko, Gorana Gašljević, Nina Kovačević, Maša Omerzel, Gregor Serša, Sebastjan Merlo, Maja Čemažar, 2023, izvirni znanstveni članek Povzetek: Background. Electrochemotherapy has good local effectiveness in the treatment of vulvar cancer. Most studies have reported the safety and effectiveness of electrochemotherapy for palliative treatment of gynecological cancers and mostly vulvar squamous cell carcinoma. Some tumors, however, fail to respond to electrochemotherapy. The biological features/determinants for the nonresponsiveness are not determined yet. Patient and methods. A recurrence of vulvar squamous cell carcinoma was treated by electrochemotherapy using intravenous administration of bleomycin. The treatment was performed by hexagonal electrodes according to standard operating procedures. We analyzed the factors that could determine nonresponsiveness to electrochemotherapy. Results. Based on the presented case of nonresponsive vulvar recurrence to electrochemotherapy, we hypothesize that the vasculature of the tumors prior to treatment may predict the response to electrochemotherapy. The histological analysis showed minimal presence of blood vessels in the tumor. Thus, low perfusion may reduce drug delivery and lead to a lower response rate because of the minor antitumor effectiveness of vascular disruption. In this case, no immune response in the tumor was elicited by electrochemotherapy. Conclusions. In this case, of nonresponsive vulvar recurrence treated by electrochemotherapy, we analyzed possible factors that could predict treatment failure. Based on histological analysis, low vascularization of the tumor was observed, which hampered drug delivery and distribution and resulted in no vascular disrupting action of electrochemotherapy. All these factors could contribute to ineffective treatment with electrochemotherapy.
Ključne besede: electrochemotherapy, bleomycin, vulvar cancer
Objavljeno v DiRROS: 25.07.2024; Ogledov: 203; Prenosov: 121
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19. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: Deinococcus-Thermus, Deinococcaceae, Deinococcus ficus, radiation-resistant, rod-shaped, phenotype characterization, genome analysis, phylogenetic analysis
Objavljeno v DiRROS: 25.07.2024; Ogledov: 228; Prenosov: 160
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20. 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, izvirni znanstveni članek Povzetek: 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.
Objavljeno v DiRROS: 25.07.2024; Ogledov: 177; Prenosov: 153
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