1. A five-step framework for creating forests for the futureMarko Kovač, Gregor Božič, Andreja Ferreira, Gal Kušar, Boštjan Mali, 2024, izvirni znanstveni članek Povzetek: Changing environmental conditions, disturbances, and escalating demands for forest ecosystem services require foresters to restore present forestlands with new forest generations that will exhibit ecological integrity, diversity, high adaptive capacity, and the ability to provide essential ecosystem services. Establishing such forests requires careful consideration of the forest landscape and site dynamics. In pursuit of these requirements, we developed a novel framework that enables the restoration of forest sites and promotes the desired features of the forest complex at the same time. This framework was designed with the methods of system engineering and was organized in the same way as the forest planning process. It was tested in the habitat type of Illyrian Fagus sylvatica forests belonging to the Natura 2000 network. The environmental, vegetation, and site conditions were investigated via field inspections, available forest management plans, and simple GIS analyses. Additionally, we established a seminatural stand composed of European beech, sessile oak, sycamore maple, silver fir, and some wild fruit tree species. The survival of planted species was assessed using census and simple random sampling, the performance of provenances by the Student’s test, while microhabitat factors were explored by a one-way ANOVA. The survival rate of key species was estimated to be 55.6%, while that of fruit species was estimated to be 94.5%. Our framework demonstrated satisfactory performance and contained sufficient benchmarks to facilitate consistent decision-making. In the discussion, we elucidate the framework’s primary features and attributes of the mixed stand, where we also expose some open issues to be addressed in the future.
Ključne besede: restoration, forest habitat type, indigenous species, planting, mixed stand, key species, fruit species
Objavljeno v DiRROS: 13.06.2024; Ogledov: 10; Prenosov: 5
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2. Evidence-based unification of potato gene models with the UniTato collaborative genome browserMaja Zagorščak, Jan Zrimec, Carissa Bleker, Nadja Francesca Nolte, Mojca Juteršek, Živa Ramšak, Kristina Gruden, Marko Petek, 2024, izvirni znanstveni članek Povzetek: Potato (Solanum tuberosum) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, and despite frequent updates, they are not unified. This hinders the comparison of gene models across versions, limits the ability to reuse experimental data without significant re-analysis, and leads to missing or wrongly annotated genes. Here, we unify the recent potato double monoploid v4 and v6 gene models by developing an automated merging protocol, resulting in a Unified poTato genome model (UniTato). We subsequently established an Apollo genome browser (unitato.nib.si) that enables public access to UniTato and further community-based curation. We demonstrate how the UniTato resource can help resolve problems with missing or misplaced genes and can be used to update or consolidate a wider set of gene models or genome information. The automated protocol, genome annotation files, and a comprehensive translation table are provided at github.com/NIB-SI/unitato.
Ključne besede: bioinformatics analysis, plant genome annotation, gene model annotations, Phureja group, GFF files, poTato genome model, UniTato
Objavljeno v DiRROS: 11.06.2024; Ogledov: 35; Prenosov: 38
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3. Stress knowledge map : a knowledge graph resource for systems biology analysis of plant stress responsesCarissa Bleker, Živa Ramšak, Andras Bittner, Vid Podpečan, Maja Zagorščak, Bernhard Wurzinger, Špela Baebler, Marko Petek, Maja Križnik, Anže Županič, Kristina Gruden, 2024, izvirni znanstveni članek Povzetek: Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
Ključne besede: Stress knowledge map, knowledge graph, knowledge network, entry point, plant digital twin, plant stress responses, plant signaling, systems biology
Objavljeno v DiRROS: 11.06.2024; Ogledov: 31; Prenosov: 23
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5. Electrochemotherapy with bleomycin of different types of cutaneous tumours in a ferret (Mustela putorius furo)Joško Račnik, Tanja Švara, Marko Zadravec, Mitja Gombač, Maja Čemažar, Gregor Serša, Nataša Tozon, 2018, izvirni znanstveni članek Povzetek: Mast cell tumour, sebaceous gland adenoma, and less common squamous papilloma are skin tumours in ferrets (Mustela putorius furo), and early excisional surgery is usually the treatment of choice. The aim of our study was to investigate the effectiveness of electrochemotherapy (ECT), a new, minimally invasive non-surgical method, as first treatment option of different types of ferret skin tumours located on surgically difficult sites. Materials and methods A 5-year-old castrated male ferret with two cutaneous masses, presenting 4 months apart and a 7-year-old spayed female ferret with two cutaneous masses, that appeared simultaneously on two locations are presented. In the first patient, both masses were diagnosed as mast cell tumours, and in the second patient, squamous papilloma and sebaceous adenoma were diagnosed. One session of ECT with bleomycin injected intratumourally was applied in all tumours. Results Complete response (CR) of all tumours was obtained, without recurrence during observation period of 15 months after ECT for first tumour and 11 months after ECT of the tumour located on the right hock in first patient, and 8 months after treatment for the second patient. Conclusions In present study, ECT with bleomycin proved to be safe and effective against different cutaneous tumours in ferrets. Due of good results, low cost and relatively easy procedure, ECT could be the treatment of choice instead of surgery for the selected skin tumours in ferrets.
Objavljeno v DiRROS: 11.06.2024; Ogledov: 18; Prenosov: 14
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6. Prevalence of BRAF, NRAS and c-KIT mutations in Slovenian patients with advanced melanomaMaja Ebert Moltara, Srdjan Novaković, Marko Boc, Marina Bučić, Martina Reberšek, Vesna Zadnik, Janja Ocvirk, 2018, izvirni znanstveni članek Povzetek: BRAF, NRAS and c-KIT mutations are characteristics of tumour tissues that influence on treatment decisions in metastatic melanoma patients. Mutation frequency and their correlation with histological characteristics in Slovenian population have not been investigated yet. Patients and methods. In our retrospective analysis we analysed mutational status of BRAF, NRAS and c-KIT in 230 pathological samples of patients who were intended to be treated with systemic therapy due to metastatic disease at the Institute of Oncology Ljubljana between 2013 and 2016. We collected also histological characteristics of primary tumours and clinical data of patients and correlated them with mutational status of tumour samples. Results. The study population consisted of 230 patients with a mean age 59 years (range 25%85). 141 (61.3%) were males and 89 (38.7%) females. BRAF mutations were identified in 129 (56.1%), NRAS in 31 (13.5%) and c-KIT in 3 (1.3%) tissue samples. Among the 129 patients with BRAF mutations, 114 (88.4%) patients had V600E mutation and 15 (11.6%) had V600K mutation. Patients with BRAF mutations tended to be younger at diagnosis (52 vs. 59 years, p < 0.05), patients with NRAS mutations older (61 vs. 55 years, p < 0.05). Number of c-KIT mutations were too low for any statistical correlation, but there was one out of 3 melanoma located in mucus membranes. Conclusions. The analysis detected high rate of BRAF mutations, low NRAS mutations and low c-KIT mutations compared to previously published studies in Europe and North America. One of the main reasons for this observation is specific characteristics of study population.
Ključne besede: BRAF, NRAS, c-KIT, melanoma
Objavljeno v DiRROS: 10.06.2024; Ogledov: 34; Prenosov: 28
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7. Spremljanje bolnikov z rakom po zaključenem zdravljenjuMarko Hočevar, 2024, objavljeni strokovni prispevek na konferenci Povzetek: V razvitem zahodnem svetu s staranjem populacije strmo narašča breme raka. Prevalenca raka je v zadnjih 50 letih naraščala praktično eksponentno. Bolniki po končanem primarnem zdravljenju s kurativnim namenom so bili tradicionalno spremljani v ustanovah, kjer so bili zdravljeni, in sicer pet let ali več, glavni namen spremljanja pa je bil zgodnje odkrivanje morebitne ponovitve bolezni. Po tem obdobju so bolnike prevzeli v oskrbo družinski zdravniki. Takšen tradicionalen način spremljanja bolnikov po končanem zdravljenju (angl. follow-up) zanemari vse ostale težave in potrebe preživelih z rakom. V zadnjem obdobju se zato pojavlja nov, širši pojem spremljanja bolnikov v onkologiji (angl. survivorship), ki naslavlja različne fizične, psihosocialne, materialne in informacijske težave in potrebe, ki jih imajo ti bolniki. Idealno je, da dobi vsak bolnik z rakom ob koncu zdravljenja t. i. načrt oskrbe preživelih, ki jasno povzame opravljeno zdravljenje in hkrati natančno opiše načrt spremljanja. Težave in potrebe preživelih se močno razlikujejo med različnimi vrstami raka in med različnimi načini zdravljenja, prav tako pa po posamičnih obdobjih preživetja. V prispevku so opisani različni modeli, ki so nam na voljo pri organizaciji spremljanja bolnikov v onkologiji in predlagan način stratificiranja bolnikov v različne skupine glede na verjetnost pojava poznih posledic zdravljenja in ponovitve bolezni. Najprimernejši modeli za posamezne vrste raka bodo opisani v posebnih prispevkih in bodo upoštevali specifiko posameznih rakov (npr. ginekologi na primarnem nivoju pri ginekoloških rakih). V prispevku bo dodatno poudarjen pomen umestitve poglavja o spremljanju bolnikov v onkologiji v priporočila in klinične poti za posamične vrste raka ter njihovo sprotno posodabljanje ob novih spoznanjih.
Ključne besede: bolniki, onkologija, spremljanje bolnikov
Objavljeno v DiRROS: 06.06.2024; Ogledov: 79; Prenosov: 31
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8. Characterization of micro-threaded stem taper surface of cementless hip endoprosthesesDrago Dolinar, Boštjan Kocjančič, Klemen Avsec, Barbara Šetina, Aleksandra Kocijan, Matjaž Godec, Marko Sedlaček, Mojca Debeljak, John T. Grant, Timon Zupanc, Monika Jenko, 2024, izvirni znanstveni članek Povzetek: We investigated micro-threaded stem taper surface and its impact on premature failures, aseptic loosening, and infection in cementless hip endoprostheses. Our study focused on the fretting, and crevice corrosion of micro-threaded tapers, as well as the characterization of the microstructure and surface properties of two new and three retrieved Zweymüller stem tapers. The retrieved samples were selected and examined based on the head–stem taper interface being the sole source of modularity with a metallic component, specifically between the Ti alloy taper stem and the ceramic head. To determine the surface chemistry and microstructures of both new and retrieved hip endoprostheses stem taper titanium alloy, scanning -electron microscopy (SEM) was employed for morphological and microstructural analyses. Energy dispersive spectroscopy (EDS) was utilized for characterizing chemical element distribution, and electron backscattered diffraction (EBSD) was used for phase analysis. The roughness of the micro-threated stem tapers from different manufacturers was investigated using an optical profilometer, with standard roughness parameters Ra (average surface roughness) and Rz (mean peak to valley height of the roughness profile) being measured. Electrochemical studies revealed no fretting corrosion in retrieved stem tapers with ceramic heads. Consequently, three retrieved tapers and two new ones for comparison underwent potentiodynamic measurements in Hank’s solution to determine the corrosion rate of new and retrieved stem taper surfaces. The results showed a low corrosion rate for both new and prematurely failed retrieved samples due to aseptic loosening. However, the corrosion rate was higher in infected and low-grade infected tapers. In conclusion, our study suggests that using ceramic heads reduces taper corrosion and subsequently decreases the incidence of premature failures in total hip arthroplasty.
Ključne besede: total hip arthroplasty, stem micro-threaded taper, taper surface morphology, microstructure, corrosion, Ti implant alloy
Objavljeno v DiRROS: 06.06.2024; Ogledov: 73; Prenosov: 63
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9. pISA-tree : a data management framework for life science research projects using a standardised directory treeMarko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll Rius, Špela Baebler, Kristina Gruden, 2022, izvirni znanstveni članek Ključne besede: pISA-tree, ISA model, data management, research data, metadata
Objavljeno v DiRROS: 05.06.2024; Ogledov: 89; Prenosov: 57
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10. Proximity to riverbed influences physiological response of adult pedunculate oak treesLazar Kesić, Matjaž Čater, Saša Orlović, Bratislav Matović, Marko Stojanović, Mirjana Bojović, 2023, izvirni znanstveni članek Povzetek: The pedunculate oak (Quercus robur L.) is economically and ecologically one of the most significant tree species in Serbia, however, little is known about the influence of the riverbed distance and its water supply on ecophysiological responses of this species. Given the limited information on the light-response curve of photosynthesis for oaks in southwest Srem, Serbia, the aim of this paper is to enhance understanding of their ecophysiological responses in this context. Maximum assimilation rate (Amax), the quantum yield (Ф), and light compensation point (LCP) were compared in adult trees situated along the transect from the river: (1) close to the river, (2) intermediate, (3) farthest from the river, and (4) forest reserve (second closest), with the first three transects being managed forests and the last one being an unmanaged forest reserve. The measurements were conducted in July during the first evidence of drought. The highest Amax rates were measured in all light intensities on the site closest to the river and the smallest on the site that was most distant to the water source. The most efficient were trees close to the river and the ones in the forest reserve. No significant difference between compensation points was confirmed for the studied groups of trees, although the forest reserve trees showed slightly higher values. The results demonstrated clear response between transects, which followed the distance from the riverbed. Pedunculate oak's reliance on groundwater is in tight relation with ecophysiological processes in trees; groundwater depletion may threaten its survival in areas distant from the river.
Ključne besede: Quercus robur L., floodplain forest, drought, light-response curves, transects
Objavljeno v DiRROS: 05.06.2024; Ogledov: 994; Prenosov: 48
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