21. Pridobivanje in uporaba ekstraktivov iz lesa in drevesne skorjePrimož Oven, Ida Poljanšek, Urša Osolnik, Viljem Vek, 2024, izvirni znanstveni članek Povzetek: Ekstraktivi so nizkomolekularne spojine, ki so v vseh rastlinskih tkivih, tudi v lesu in drevesni skorji. V drevesu imajo pomembne ekološke in fiziološke funkcije, obenem pa predstavljajo bioosnovane proizvode z visoko dodano vrednostjo, ki jih je mogoče pridobivati tudi iz lesa slabše kakovosti in biomasnih ostankov gozdnih lesnih verig. V prispevku bomo ekstraktive razvrstili, pojasnili, kakšna je kakovostna in količinska spremenljivost po posameznih tkivih izbranih drevesnih vrst, predstavili bomo načine pridobivanja in področja uporabe. Ocenjujemo, da je pridobivanje ekstraktivov dokaj enostaven tehnološki postopek, ki bi bil v obliki manjše biorafinerije izvedljiv v lokalnih okoljih, kjer so na voljo zadostne količine lesne biomase.
Ključne besede: les, skorja, ekstraktivi, kaskadna raba, biorafinacija
Objavljeno v DiRROS: 24.07.2024; Ogledov: 19; Prenosov: 2
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22. Inter-laboratory assessment of different digital PCR platforms for quantification of human cytomegalovirus DNAJernej Pavšič, Alison S. Devonshire, Andrej Blejec, Carole A. Foy, Fran Van Heuverswyn, Gerwyn M. Jones, Heinz Schimmel, Jana Žel, Jim F. Huggett, Nicholas Redshaw, Maria Karczmarczyk, Erkan Mozioglu, Sema Akyürek, Müslüm Akgöz, Mojca Milavec, 2017, izvirni znanstveni članek Povzetek: Quantitative PCR (qPCR) is an important tool in pathogen detection. However, the use of different qPCR components, calibration materials and DNA extraction methods reduces comparability between laboratories, which can result in false diagnosis and discrepancies in patient care. The wider establishment of a metrological framework for nucleic acid tests could improve the degree of standardisation of pathogen detection and the quantification methods applied in the clinical context. To achieve this, accurate methods need to be developed and implemented as reference measurement procedures, and to facilitate characterisation of suitable certified reference materials. Digital PCR (dPCR) has already been used for pathogen quantification by analysing nucleic acids. Although dPCR has the potential to provide robust and accurate quantification of nucleic acids, further assessment of its actual performance characteristics is needed before it can be implemented in a metrological framework, and to allow adequate estimation of measurement uncertainties. Here, four laboratories demonstrated reproducibility (expanded measurement uncertainties below 15%) of dPCR for quantification of DNA from human cytomegalovirus, with no calibration to a common reference material. Using whole-virus material and extracted DNA, an intermediate precision (coefficients of variation below 25%) between three consecutive experiments was noted. Furthermore, discrepancies in estimated mean DNA copy number concentrations between laboratories were less than twofold, with DNA extraction as the main source of variability. These data demonstrate that dPCR offers a repeatable and reproducible method for quantification of viral DNA, and due to its satisfactory performance should be considered as candidate for reference methods for implementation in a metrological framework.
Ključne besede: digital PCR, DNA quantification, inter-laboratory assessment, human cytomegalovirus, virus reference materials
Objavljeno v DiRROS: 24.07.2024; Ogledov: 8; Prenosov: 5
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23. Učinkovitost zatiranja invazivne tujerodne vrste navadne barvilnice : poraba časa in potencialne izboljšave pri negi mladjaPeter Smolnikar, Urban Žitko, Marija Kolšek, Matevž Triplat, 2024, izvirni znanstveni članek Povzetek: V svetu invazivne tujerodne vrste rastlin (ITVR) povzročajo mnoge spremembe v okolju. Za zatiranje ITVR je znanih precej metod, primernost posamezne in posledično tudi uspešnost pa sta odvisni od vsakega primera posebej – predvsem od cilja, ki ga želimo doseči z zatiranjem. V študiji smo spremljali zatiranje navadne barvilnice v okviru nege mladja, tj. z rezjo pri tleh. Študija je potekala na objektu s površino 2,82 ha, dela so izvajali trije delavci. Cilji študije so bili ugotoviti porabo časa na površino in pridobiti manjkajoča znanja na področju izvajanja dodatnih ukrepov pri negi mladja. V povprečju so delavci za en hektar obžetve potrebovali 18,8 ure produktivnega časa. Po simulaciji študije na osemurni delavnik faktor neproduktivnega časa znaša 1,39 (σ = 0,053) in je nižji od priznanega državnega faktorja neproduktivnega časa (1,58) za sečnjo. Pri interpretaciji rezultatov je potrebna previdnost, ker so pri kratkotrajnih (manj obsežnih) študijah pogosto podcenjeni faktorji neproduktivnega časa. Teoretični izračun, ki temelji na linearni regresiji podatkov, kaže, da je za obžetev enega hektara v celoti potrebno okrog dvaindvajset ur. Kljub že tako nizkemu faktorju neproduktivnega časa je še rezerva za optimizacijo delovnega procesa, vendar so za to potrebne dolgotrajnejše in obsežnejše študije časa.
Ključne besede: gozdarstvo, invazivne rastline, zatiranje, nega pomladka, časovna študija, Phytolacca americana
Objavljeno v DiRROS: 24.07.2024; Ogledov: 17; Prenosov: 2
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24. Usmerjanje obnove, nege in varstva gozdovaBoris Rantaša, Aleš Poljanec, 2024, predgovor, uvodnik, spremna beseda Ključne besede: obnova načrtov, gospodarjenje z gozdovi, nega gozdov, varstvo gozdov
Objavljeno v DiRROS: 24.07.2024; Ogledov: 14; Prenosov: 5
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26. Cathepsin K cleavage of SDF-1[alpha] inhibits its chemotactic activity towards glioblastoma stem-like cellsVashendriya V. V. Hira, Urška Verbovšek, Barbara Breznik, Matic Srdič, Marko Novinec, Hala Kakar, Jill Wormer, Britt van der Swaan, Brigita Lenarčič, Luiz Juliano, Shwetal Mehta, Cornelis J. F. van Noorden, Tamara Lah Turnšek, 2017, izvirni znanstveni članek Povzetek: Glioblastoma (GBM) is the most aggressive primary brain tumor with poor patient survival that is at least partly caused by malignant and therapy-resistant glioma stem-like cells (GSLCs) that are protected in GSLC niches. Previously, we have shown that the chemo-attractant stromal-derived factor-1α (SDF-1α), its C-X-C receptor type 4 (CXCR4) and the cysteine protease cathepsin K (CatK) are localized in GSLC niches in glioblastoma. Here, we investigated whether SDF-1α is a niche factor that through its interactions with CXCR4 and/or its second receptor CXCR7 on GSLCs facilitates their homing to niches. Furthermore, we aimed to prove that SDF-1α cleavage by CatK inactivates SDF-1α and inhibits the invasion of GSLCs. We performed mass spectrometric analysis of cleavage products of SDF-1α after proteolysis by CatK. We demonstrated that CatK cleaves SDF-1α at 3 sites in the N-terminus, which is the region of SDF-1α that binds to its receptors. Confocal imaging of human GBM tissue sections confirmed co-localization of SDF-1α and CatK in GSLC niches. In accordance, 2D and 3D invasion experiments using CXCR4/CXCR7-expressing GSLCs and GBM cells showed that SDF-1α had chemotactic activity whereas CatK cleavage products of SDF-1α did not. Besides, CXCR4 inhibitor plerixafor inhibited invasion of CXCR4/CXCR7-expressing GSLCs.
In conclusion, CatK can cleave and inactivate SDF-1α. This implies that CatK activity facilitates migration of GSLCs out of niches. We propose that activation of CatK may be a promising strategy to prevent homing of GSLCs in niches and thus render these cells sensitive to chemotherapy and radiation.
Ključne besede: glioma stem-like cells, niche, stromal derived factor-[alpha], cathepsin K
Objavljeno v DiRROS: 24.07.2024; Ogledov: 14; Prenosov: 6
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27. Testing the influence of sediment granulometry on heterotrophic respiration with a new laboratory flow-through systemNataša Mori, Barbara Debeljak, David Kocman, Tatjana Simčič, 2017, izvirni znanstveni članek Povzetek: 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.
Ključne besede: carbon fluxes, freshwaters, geomorphology, hyporheic zone, respiration, sediments
Objavljeno v DiRROS: 24.07.2024; Ogledov: 14; Prenosov: 7
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28. Rapid loop-mediated isothermal amplification assays for grapevine yellows phytoplasmas on crude leaf-vein homogenate has the same performance as qPCRPolona Kogovšek, Nataša Mehle, Anja Pugelj, Tjaša Jakomin, Hans-Josef Schroers, Maja Ravnikar, Marina Dermastia, 2017, izvirni znanstveni članek Povzetek: A fluorescence-based real-time loop-mediated isothermal amplification (LAMP) assay for ‘Candidatus Phytoplasama solani’ (Bois noir phytoplasma; BNp) detection was developed and optimised for rapid laboratory and on-site BNp detection. This assay is highly specific, rapid and as sensitive as qPCR. It was validated according to European and Mediterranean Plant Protection Organisation recommendations. In addition, 286 grapevine leaf samples from the 2015 growing season were tested with this new real-time LAMP assay and an assay previously developed for detection of Flavescence dorée phytoplasma (FDp). These LAMP assays for detection of both BNp and FDp used without any DNA extraction step, which is a required step for qPCR analysis, were comparably effective to qPCR, and positive results were obtained in less than 35 min.
Ključne besede: real-time LAMP, grapevine yellows phytoplasma, validation
Objavljeno v DiRROS: 24.07.2024; Ogledov: 18; Prenosov: 7
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29. Identification of women with high grade histopathology results after conisation by artificial neural networksMarko Mlinarič, Miljenko Križmarić, Iztok Takač, Alenka Repše-Fokter, 2022, izvirni znanstveni članek Povzetek: Background: The aim of the study was to evaluate if artificial neural networks can predict high-grade histopathology results after conisation from risk factors and their combinations in patients undergoing conisation because of pathological changes on uterine cervix. Patients and methods: We analysed 1475 patients who had conisation surgery at the University Clinic for Gynaecology and Obstetrics of University Clinical Centre Maribor from 1993-2005. The database in different datasets was arranged to deal with unbalance data and enhance classification performance. Weka open-source software was used for analysis with artificial neural networks. Last Papanicolaou smear (PAP) and risk factors for development of cervical dysplasia and carcinoma were used as input and high-grade dysplasia Yes/No as output result. 10-fold cross validation was used for defining training and holdout set for analysis. Results: Baseline classification and multiple runs of artificial neural network on various risk factors settings were performed. We achieved 84.19% correct classifications, area under the curve 0.87, kappa 0.64, F-measure 0.884 and Matthews correlation coefficient (MCC) 0.640 in model, where baseline prediction was 69.79%. Conclusions: With artificial neural networks we were able to identify more patients who developed high-grade squamous intraepithelial lesion on final histopathology result of conisation as with baseline prediction. But, characteristics of 1475 patients who had conisation in years 1993-2005 at the University Clinical Centre Maribor did not allow reliable prediction with artificial neural networks for every-day clinical practice.
Ključne besede: artificial neural networks, conisation, uterine cervical cancer, uterine cervical dysplasia, displazija materničnega vratu, rak materničnega vratu, konizacija, umetne nevronske mreže
Objavljeno v DiRROS: 24.07.2024; Ogledov: 14; Prenosov: 7
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