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1.
Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbellii
Neža Orel, Eduard Fadeev, Gerhard J. Herndl, Valentina Turk, Tinkara Tinta, 2024, izvirni znanstveni članek

Povzetek: Background: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. Results: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. Conclusions: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
Ključne besede: whole-genome assembly, non-axenic culture, plasmid, marine bacteria, marine biology
Objavljeno v DiRROS: 28.03.2024; Ogledov: 1; Prenosov: 0
URL Povezava na datoteko

2.
Recombinant human erythropoietin alters gene expression and stimulates proliferation of MCF-7 breast cancer cells
Nina Trošt, Tina Stepišnik, Sabina Berne, Anja Pucer Janež, Toni Petan, Radovan Komel, Nataša Debeljak, 2013, objavljeni znanstveni prispevek na konferenci

Povzetek: Background. Functional erythropoietin (EPO) signaling is not specific only to erythroid lineages and has been confirmed in several solid tumors, including breast. Three different isoforms of erythropoietin receptor (EPOR) have been reported, the soluble (EPOR-S) and truncated (EPOR-T) forms acting antagonistically to the functional EPOR. In this study, we investigated the effect of human recombinant erythropoietin (rHuEPO) on cell proliferation, early gene response and the expression of EPOR isoforms in the MCF-7 breast cancer cell line.Materials and methods. The MCF-7 cells were cultured with or without rHuEPO for 72 h or 10 weeks and assessed for their growth characteristics, expression of early response genes and different EPOR isoforms. The expression profile of EPOR and EPOR-T was determined in a range of breast cancer cell lines and compared with their invasive properties.Results. MCF-7 cell proliferation after rHuEPO treatment was dependent on the time of treatment and the concentration used. High rHuEPO concentrations (40 U/ml) stimulated cell proliferation independently of a preceding long-term exposure of MCF-7 cells to rHuEPO, while lower concentrations increased MCF-7 proliferation only after 10 weeks of treatment. Gene expression analysis showed activation of EGR1 and FOS, confirming the functionality of EPOR. rHuEPO treatment also slightly increased the expression of the functional EPOR isoform, which, however, persisted throughout the 10 weeks of treatment. The expression levels of EPOR-T were not influenced. There were no correlations between EPOR expression and the invasiveness of MCF-7, MDA-MB-231, Hs578T, Hs578Bst, SKBR3, T-47D and MCF-10A cell lines.Conclusions. rHuEPO modulates MCF-7 cell proliferation in time- and concentration-dependent manner. We confirmed EGR1, FOS and EPOR as transcription targets of the EPO-EPOR signaling loop, but could not correlate the expression of different EPOR isoforms with the invasiveness of breast cancer cell lines.
Ključne besede: breast cancer, erythropoietin, gene expression
Objavljeno v DiRROS: 22.03.2024; Ogledov: 51; Prenosov: 24
.pdf Celotno besedilo (850,15 KB)
Gradivo ima več datotek! Več...

3.
Improved survival after introduction of chemotherapy for malignant pleural mesothelioma in Slovenia : population-based survey of 444 patients
Viljem Kovač, Matjaž Zwitter, Tina Žagar, 2012, izvirni znanstveni članek

Povzetek: Background. Malignant pleural mesothelioma is a rare tumour with increasing frequency throughout the world. Due to long latency after exposure to asbestos, restrictions in the production and use of asbestos have not yet alleviated the burden of mesothelioma. During the last decade, several trials confirmed the benefit of systemic treatment with drugs such as doublets with cisplatina and gemcitabine or pemetrexed for carefully selected patients in good performance status. The purpose of this survey was to assess the impact of systemic treatment for the whole national population of patients with mesothelioma. Patients and methods. A retrospective study included all patients in Slovenia with histologically confirmed diagnosis of malignant pleural mesothelioma in the period from 1974 till 2008. Data from the Cancer Registry of Slovenia were supplemented by review of clinical records of the Institute of Oncology in Ljubljana where virtually all non-surgical treatment for mesothelioma was performed. We analysed the incidence, treatment, and survival of patients treated in the era of infrequent chemotherapy (1974-2003,the first period) and after it (2004-2008, the second period). Results. The survey included 444 patients, of whom 325 and 119 were diagnosed in the first and second period, respectively. Joinpoint regression analysis showed that after 1995 the trend in crude incidence rates increased more rapidly; the annual change was 0.03 per 100,000 per year before 1995 and 0.06 per 100,000 per year after. There was clear male predominance (70%) throughout the period covered by the survey. The proportion of patients above 65 years of age increased from 41.8% to 54.6% for the first and second period, respectively (p = 0.02). With a total of 52 (11.7%) operated patients, surgical treatment was rare and used only for selected patients with early disease and without comorbidity, leading to their relatively long median survival of 13.6 months. Chemotherapy was applied to 56 (17.2%) and to 96 (80.7%) patients during the first and second period, respectively. While a variety of older drugs were used in the first period, the most common regimen in the second period (applied to 91 patients) was doublet of low-dose gemcitabine in prolonged infusion and cisplatin. For the whole population of patients regardless the mode of treatment, median survival was 7.4 and 12.6 months (p-value = 0.037) for the first and second period, respectively. Conclusions. Increasing incidence, male predominance and increased proportion of older patients confirm that the burden of mesothelioma persists in spite o fa 15-years old ban in the production of asbestos. Modern chemotherapy, and in particular treatment with low-dose gemcitabine in prolonged infusion and cisplatin significantly prolonged median survival of patients with malignant pleural mesothelioma in Slovenia.
Objavljeno v DiRROS: 21.03.2024; Ogledov: 57; Prenosov: 21
.pdf Celotno besedilo (588,42 KB)

4.
Is there any progress in routine management of lung cancer patients? A comparative analysis of an institution in 1996 and 2006
Lučka Debevec, Tina Jerič, Viljem Kovač, Marko Bitenc, Mihael Sok, 2009, izvirni znanstveni članek

Povzetek: Background. The aim of the study was to establish eventual progress in routine management of lung cancer patients over a ten-year period at University Clinic for Respiratory and Allergic Diseases Golnik, Slovenia, comparing the results of analysis of 345 patients, diagnosed in 1996 (with analysis performed in 2002), and 405 patients, diagnosed in 2006 (with analysis performed in 2008).Patients and methods. The patients of both analysed groups were of comparable age and number of patients in stage I and II, but there were relatively more females, patients with better performance status, more precise clinical staging and tumour histology in the 2006 group. The parameters used for assessing the progress of management were as follows: time period from admittance to diagnosis and to surgery; precision of staging; accordance of clinical and pathological staging in resected patients; percentage of exploratory thoracotomy; and use of new treatment modalities. The proportion of patients in selected/actual primary treatment modality and survival rate could also be used for assessing the progress. Results. Althoughunessential longer time from admittance to microscopic confirmed diagnosis increased from a mean 7.4 to 8.6 days in 2006 progress was established by the following: more precise clinical staging (stage I and II also A and B stage, TNM staging also in small-cell lung cancer patients); improved accordance with clinical and pathological staging in resected patients (46% against 58%); decreased percentage of exploratory thoracotomy (13% against 4%); increased use of multimodality therapy as primary treatment modality (radiotherapy/chemotherapy, neoadjuvant chemotherapy); newly performed radio frequency tumour ablation. The proportion in selected/actual surgery increased from 76% to 93% and median survival rate of all patients from 6.2 to 10.6 months. (Abstract truncated at 2000 characters)
Objavljeno v DiRROS: 08.03.2024; Ogledov: 70; Prenosov: 22
.pdf Celotno besedilo (80,75 KB)

5.
Ecotoxicologically relevant cyclic peptides from cyanobacterial bloom (Planktothrix rubecens) - a threat to human and environmental health
Bojan Sedmak, Tina Eleršek, Olga Grach-Pogrebinsky, Shmuel Carmeli, Nataša Sever, Tamara Lah Turnšek, 2008, izvirni znanstveni članek

Povzetek: Background. The information of the overall production of major cyanobacterial cyclic peptides in a water body is essential for risk assessment and for the prediction of future development of the bloom. A procedure that gives a reviewof both toxic and non-hepatotoxic hydrophilic cyclic peptide production is important to evaluate the ecological conditions in the water environment and to predict the release of dangerous toxic and tumour promoting substances.Methods. The cyclic peptides were identified on the basis of their retention times, characteristic spectra, molecular masses and biological activity. The non-hepatotoxic cyclic peptides were characterised by their inhibition of porcine pancreatic elastase, while cytotoxicity to mammalian cells was tested with the MTT test on B16 cell line. Conclusions. The method presented gives a rapid, simultaneous assessment, preliminary identification and estimation of bioactive cyclic peptides. The synthesis of non-hepatotoxic cyclic peptides can mediate the release various toxic and otherwise biologically active substances that induce systemic genotoxicity in mammals.
Ključne besede: tumor promoters, microcystin, anabaenopeptin, planktopeptin, toxic cyanobacterial blooms, environmental health
Objavljeno v DiRROS: 07.03.2024; Ogledov: 83; Prenosov: 13
.pdf Celotno besedilo (286,29 KB)

6.
Na Krasu sadilo več kot 1300 prostovoljcev
Tina Dolenc, 2023, poljudni članek

Ključne besede: pogozdovanje, Kras, prostovoljci, gozdni požari
Objavljeno v DiRROS: 29.02.2024; Ogledov: 79; Prenosov: 0
.pdf Celotno besedilo (265,60 KB)

7.
Sejanje z droni na težko dostopnih terenih
Tina Dolenc, 2023, strokovni članek

Ključne besede: pogozdovanje, brezpilotni letalniki, obnova gozdov
Objavljeno v DiRROS: 29.02.2024; Ogledov: 88; Prenosov: 0
.pdf Celotno besedilo (206,39 KB)

8.
Že 25. izbrali najbolj skrbne lastnike gozdov
Tina Dolenc, 2023, strokovni članek

Ključne besede: propaganda, lastniki gozdov, priznanja najbolj skrbnim lastnikom gozdov
Objavljeno v DiRROS: 29.02.2024; Ogledov: 93; Prenosov: 2
.pdf Celotno besedilo (135,36 KB)

9.
Incidenca raka v prvem letu epidemije covida-19
Vesna Zadnik, Tina Žagar, Nika Bric, Mojca Birk, Amela Duratović Konjević, Ana Mihor, Katarina Lokar, Sonja Tomšič, 2023, strokovni članek

Povzetek: Uvod: Število novih diagnoz raka (incidenca) se v Sloveniji v zadnjem desetletju povečuje za povprečno 1,6 % na leto. V letu 2020, prvem letu omejitvenih ukrepov zaradi epidemije covida19, smo s platformo OnKOvid predvideli 3–8-odstotni padec novih diagnoz raka. Namen je predstaviti uradno incidenco raka za Slovenijo za leto 2020 in ugotoviti, kolikšen je bil dejansko manko novih diagnoz raka. Metode: V Registru raka Republike Slovenije smo v skladu z mednarodnimi pravili registrirali vse nove primere raka pri prebivalcih s stalnim prebivališčem v Sloveniji. Primerjali smo jih z registrirano incidenco za 2019, modelno incidenco za 2020, preliminarnimi rezultati OnKovida in dostopnimi rezultati incidence iz registrov raka iz drugih držav. Rezultati: V letu 2020 je za rakom zbolelo 15.096 oseb v Sloveniji (7.034 žensk, 8.002 moška). Glede na modelno oceno incidence za leto 2020 gre za manko 1.854 oseb (10,9 %; 11,6 % žensk, 10,4 % moških). Pri tem je za 10,5 % manj ugotovljenih rakov v omejenem stadiju, najbolj izrazito v starosti 50–69 let (za 13,2 %). Upad je primerljiv s poročili iz Anglije, ZDA in Kanade ter deloma večji kot na Škotskem in Švedskem. Najbolj izrazit upad novih diagnoz raka ugotavljamo pri nemelanomskem kožnem raku (23 %, najbolj po 50. letu), raku prostate (15,9 %, najbolj v omejenem stadiju), pljučnem raku (8,9 %, 60–64 let, v razširjenem stadiju), raku dojk (8,3 %, 45–64 let), ne-Hodgkinovem limfomu (9 %) in levkemijah (11,6 %). Pri kožnem melanomu, raku debelega črevesa in danke ni bilo primanjkljaja. Zaključek: Upad incidence raka v letu 2020 gre verjetno na račun omejitvenih ukrepov, reorganizacije zdravstva in z zdravjem povezanega vedenja med epidemijo covida-19, beležijo jo v več državah. Med epidemijami je potrebno nemoteno izvajanje onkologije.
Ključne besede: rak, incidenca, register raka, epidemija, covid-19
Objavljeno v DiRROS: 26.02.2024; Ogledov: 121; Prenosov: 23
.pdf Celotno besedilo (301,68 KB)

10.
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