Search the repository

A+ | A- | | SLO | ENG

Abstract: The presence of plastics in the environment is currently one of the most pressing global environmental problems. Microorganisms start to form biofilms on plastic surfaces when they first come in contact with the biosphere; however, these interactions and processes are little understood, especially in freshwaters. This study aimed to better understand the colonization process of microorganisms from activated sludge on plastic materials exhibiting different surface characteristics. We inoculated synthetic fabric (PET), water bottles (PET), and plastic bags for packing vegetables and fruits (HDPE) with microorganisms from activated sludge. Mixtures of plastics and activated sludge, as well as the control, were incubated at 22-24°C in Bushnell Haas (BH) liquid medium and shaken at 120 rpm for two months. The mixtures were sub-sampled weekly and seeded into fresh BH medium with test plastic materials to avoid feeding microorganisms on dead biomass. The colonization was followed by measuring optical density (OD600) of liquid medium, by measurements of isotopic composition of carbon (δ13C) in untreated and treated plastic materials and, with in-specting the plastics surface with scanning electron microscopy (SEM). Overall, the study confirmed differences between colonizing microorganisms on different plastic material when comparing SEM micrographs of materials from the flasks inoculated with activated sludge. The texture of the HDPE bag changed during the experiment in both, control and inoculated flasks, but it is not clear whether the observed changes were due to abiotic or biotic factors. We concluded that microorganisms from activated sludge are capable of colonizing both PET and HDPE materials, and biofilm formation is most probably influenced by the chemical composition of plastics and their surface characteristics.
Keywords: biofilm, plastics, SEM, isotopic composition of carbon, co-cultivation, UV sterilization
Published in DiRROS: 31.07.2024; Views: 261; Downloads: 193
Full text (678,88 KB)
This document has many files! More...

Abstract: Background. We preformed a Phase IV non-interventional study to assess KRAS, NRAS and BRAF status in metastatic colorectal cancer (mCRC) patients suitable for 1st line treatment and to evaluate the decisions for 1st line treatment considering the treatment goals in the RAS wild type (wt) patients. The aim of our study was also to evaluate the influ-ence of a waiting period for biomarkers analysis on the start of first-line treatment.Patients and methods. Patients with histologically confirmed mCRC adenocarcinoma suitable for first-line treat-ment fulfilling all inclusion criteria were included in the study. The KRAS, NRAS and BRAF analysis was performed from tissue samples of primary tumor site or metastatic site. All included patients have given consent to participate in the study by signing the informed consent form. Results. From April 2013 to March 2018 at the Institute of Oncology Ljubljana 650 patients were included, 637 of them were treated with first- line systemic treatment according to RAS and BRAF status. Remaining 13 patients with mCRC did not receive systemic first-line treatment. The distribution of patients with KRAS mutated and wild-type tumors, was almost equal, 48.8% and 47.9% respectively, 89 % of the patients had wt NRAS tumours and 86.1% had wt BRAF tu-mours. The most frequently prescribed treatment was bevacizumab-based therapy (53.1%), either in combination with doublet chemotherapy or with mono-chemotherapy. EGFR inhibitors cetuximab and panitumumab were prescribed in wt RAS mCRC patients (30.9%). The waiting period for biomarkers analysis was two weeks.Conclusions. Our real-world data, single centre 5-year analysis showed that the distribution between wild type and mutated type tumors of the patients with mCRC was approximately the same, as worldwide, so the Slovenian popula-tion with mCRC has the same ratio distribution of KRAS, NRAS and BRAF wild and mutated genes. We concluded that a two-week waiting period for biomarkers analysis did not influence the first line treatment decision, so it was in the accordance with the worldwide treatment guidelines based on evidence-based medicine.
Keywords: metastatic colorectal cancer, RAS and BRAF biomarkers, systemic treatment
Published in DiRROS: 25.07.2024; Views: 197; Downloads: 84
Full text (367,23 KB)

Abstract: Soft rot pathogenic bacteria from the genus Dickeya cause severe economic losses in orchid nurseries worldwide, and there is no effective control currently available. In the last decade, the genus Dickeya has undergone multiple changes as multiple new taxa have been described, and just recently a new putative Dickeya species was reported. This study reports the isolation of three bacteriophages active against putative novel Dickeya spp. isolates from commercially produced infected orchids that show variable host-range profiles. Bacteriophages were isolated through enrichment from Dickeya-infected orchid tissue. Convective interaction media monolith chromatography was used to isolate bacteriophages from wastewaters, demonstrating its suitability for the isolation of infective bacteriophages from natural sources. Based on bacteriophage morphology, all isolated bacteriophages were classified as being in the order Caudovirales, belonging to three different families, Podoviridae, Myoviridae, and Siphoviridae. The presence of three different groups of bacteriophages was confirmed by analyzing the bacteriophage specificity of bacterial hosts, restriction fragment length polymorphism and plaque morphology. Bacteriophage BF25/12, the first reported Podoviridae bacteriophage effective against Dickeya spp., was selected for further characterization. Its genome sequence determined by next-generation sequencing showed limited similarity to other characterized Podoviridae bacteriophages. Interactions among the bacteriophages and Dickeya spp. were examined using transmission electron microscopy, which revealed degradation of electron-dense granules in response to bacteriophage infection in some Dickeya strains. The temperature stability of the chosen Podoviridae bacteriophage monitored over 1 year showed a substantial decrease in the survival of bacteriophages stored at -20∘C over longer periods. It showed susceptibility to low pH and UV radiation but was stable in neutral and alkaline pH. Furthermore, the stability of the tested bacteriophage was also connected to the incubation medium and bacteriophage concentration at certain pH values. Finally, the emergence of bacteriophage-resistant bacterial colonies is highly connected to the concentration of bacteriophages in the bacterial environment. This is the first report on bacteriophages against Dickeya from the Podoviridae family to expand on potential bacteriophages to include in bacteriophage cocktails as biocontrol agents. Some of these bacteriophage isolates also showed activity against Dickeya solani, an aggressive strain that causes the soft rot of potatoes, which indicates their broad potential as biocontrol agents.
Keywords: bacteriophages, genome sequencing, resistance development, convective interaction media monolith chromatography
Published in DiRROS: 25.07.2024; Views: 234; Downloads: 177
Full text (4,34 MB)
This document has many files! More...

Abstract: Treatment of early-stage non-small cell lung cancer (NSCLC) is rapidly evolving. When introducing novelties, real-life data on effectiveness of currently used treatment strategies are needed. The present study evaluated outcomes of stage I–IIIA NSCLC patients treated with upfront radical surgery in everyday clinical practice, between 2010–2017. Data of 539 consecutive patients were retrieved from a prospective hospital-based registry. All diagnostic, treatment and follow-up procedures were performed at the same thoracic oncology centre according to the valid guidelines. The primary outcome was overall survival (OS) analysed by clinical(c) and pathological(p) TNM (tumour, node, metastases) stage. The impact of clinicopathological characteristics on OS was evaluated using univariable (UVA) and multivariable regression analysis (MVA). With a median follow-up of 53.9 months, median OS and 5-year OS rate in the overall population were 90.4 months and 64.4%. Five-year OS rates by pTNM stage I, II and IIIA were 70.2%, 60.21%, and 49.9%, respectively. Both cTNM and pTNM stages were associated with OS; but only pTNM retained its independent prognostic value (p = 0.003) in MVA. Agreement between cTNM and pTNM was 69.0%. Next to pTNM, age (p = 0.001) and gender (p = 0.004) retained their independent prognostic value for OS. The study showed favourable outcomes of resectable stage I–IIIA NSCLC treated with upfront surgery in real-life. Relatively low agreement between cTNM and pTNM stages and independent prognostic value of only pTNM, observed in real-life data, suggest that surgery remains the most accurate provider of the anatomical stage of disease and important upfront therapy.
Keywords: resectable NSCLC, upfront surgery, real-life data, overall survival, prognostic factors
Published in DiRROS: 25.07.2024; Views: 199; Downloads: 164
Full text (747,28 KB)
This document has many files! More...

Abstract: Purpose Increased sedimentation due to land use intensification is increasingly affecting carbon processing in streams and rivers around the globe. This study describes the design of a laboratory-scale flow-through incubation system as a tool for the rapid estimation of sediment respiration. The measurements were compared with those obtained using an in situ closed chamber respiration method. The influence of sediment size on respiration rates was also investigated. Materials and methods Measurements were conducted on a pre-alpine gravel-bed river sediment separated into the following grain size fractions: > 60 mm (14.3%), 60–5 mm (60.2%), 5–2 mm (13.7%), 2–0.063 mm (11.1%) and <0.063 mm (0.6%). Concurrently, in situ and laboratory measurements were carried out on a naturally heterogeneous sediment. In situ respiration was determined in closed chambers as O2 consumption over time, while in the laboratory, respiration was determined using flow-through respiration chambers. Oxygen concentrations were measured using a fibre-optic oxygen meter positioned at the inflow and outflow from the chamber. Results and discussion The mean respiration rates within naturally mixed riverbed sediments were 1.27 ± 0.3 mg O2 dm−3 h−1 (n = 4) and 0.77 ± 0.1 mg O2 dm−3 h−1 (n = 3) for the flow-through chamber system and closed chamber system, respectively. Respiration rates were statistically significantly higher in the flow-through chamber system (t test, p < 0.05), indicating that closed chamber measurements underestimated the oxygen consumption within riverbed sediments. Sediment grain size was found to significantly affect respiration rates in both systems (ANOVA, p < 0.001) with the fine sediment fraction (particle size <0.063 mm) having the highest respiration rate (rflow-through = 51 ± 23 mg O2 dm−3 h−1). The smallest fractions (2–0.063 and <0.063 mm), which represent approximately 12% of total sediment volume, contributed 60% of total respiration. Conclusions The study demonstrated that flow-through respiration chambers more accurately estimate the respiration rate within riverbed sediments than in situ closed chambers, since the former experiment imitates the natural conditions where continuous interstitial flow occurs in the sediments. We also demonstrated that fine sediments (<5 mm) substantially contribute to heterotrophic respiration in the studied gravel-bed river.
Keywords: carbon fluxes, freshwaters, geomorphology, hyporheic zone, respiration, sediments
Published in DiRROS: 24.07.2024; Views: 205; Downloads: 147
Full text (1,12 MB)
This document has many files! More...