1. Water quality characteristics and source analysis of pollutants in the Maotiao river basin (SW China)Yinjiu Li, Qiuhua Li, Shulin Jiao, Chen Liu, Liuying Yang, Guojia Huang, Si Zhou, Mengshu Han, Anton Brancelj, 2022, izvirni znanstveni članek Povzetek: Rivers are an important mediator between human activities and the natural environment. They provide multiple functions, including irrigation, transportation, food supply, recreation, and water supply. Therefore, evaluations of water quality and pollution sources are of great significance for ecological restoration and management of rivers. In this study, the improved “vušekriterijumska optimizacija i kompromisno rješenje” (VIKOR in Serbian; in English: Multicriteria Optimization and Compromise Solution), and a geodetector were used to analyze the water quality characteristics and pollution sources of the Maotiao River Basin (Gizhou province, SW China). The results showed that the water quality of the Maotiao River Basin deteriorated significantly during the summer drought period, as was evident in the reservoirs and lakes. It improved in the wet season (i.e., during the summer period) due to runoff dilution. Water quality decreased along the river’s course, from upstream to downstream sections. The results of the geographic detector analysis showed that agricultural areas were the primary factor affecting the spatial distribution of water quality in the river basin. In July, August, and November 2020, the influence of agricultural land was 0.72, 0.60, or 0.80, respectively, and the interactions among urban, industrial, agricultural, and forested areas explained 99.2%, 83.2%, or 99.9% of the spatial differentiation of water quality, respectively. Due to the influence of spatial scale, settlements have a small influence on the spatial distribution of water quality. Their impact factors were 0.38, −0.24, and −0.05, respectively. Notably, the negative relationship of water quality and forested areas reflects that topography, types of landscapes, and soil thickness have considerable influences on the Maotiao River Basin’s water quality. Based on the findings, we infer that good farmland water conservancy projects and comprehensive management of different types of landscapes, such as forests, agriculture, and urban area and water bodies, are of great significance for improving water quality.
Ključne besede: water quality, statistical data, VIKOR model, CRITIC model
Objavljeno v DiRROS: 16.07.2024; Ogledov: 2; Prenosov: 4
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2. HepG2 spheroids as a biosensor-like cell-based system for (geno)toxicity assessmentMartina Štampar, Sonja Žabkar, Metka Filipič, Bojana Žegura, 2022, izvirni znanstveni članek Povzetek: 3D spheroids developed from HepG2 cells were used as a biosensor-like system for the detection of (geno)toxic effects induced by chemicals. Benzo(a)pyrene (B(a)P) and amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) with well-known mechanisms of action were used for system validation. HepG2 spheroids grown for 3 days were exposed to BaP and PhIP for 24 and 72 h. The growth and viability of spheroids were monitored by planimetry and Live/Dead staining of cells. Multi-parametric flow cytometric analysis was applied for simultaneous detection of specific end-effects including cell cycle analysis (Hoechst staining), cell proliferation (KI67 marker), and DNA double-strand breaks (ℽH2AX) induced by genotoxic compounds. Depending on the exposure concentration/time, BaP reduced spheroid growth, affected cell proliferation by arresting cells in S and G2 phase and induced DNA double-strand breaks (DSB). Simultaneous staining of ℽH2AX formation and cell cycle analysis revealed that after BaP (10 μM; 24 h) exposure 60% of cells in G0/G1 phase had DNA DSB, while after 72 h only 20% of cells contained DSB indicating efficient repair of DNA lesions. PhIP did not influence the spheroid size whereas accumulation of cells in the G2 phase occurred after both treatment times. The evaluation of DNA damage revealed that at 200 μM PhIP 50% of cells in G0/G1 phase had DNA DSB, which after 72-h exposure dropped to 40%, showing lower repair capacity of PhIP-induced DSB compared to BaP-induced. The developed approach using simultaneous detection of several parameters provides mechanistic data and thus contributes to more reliable genotoxicity assessment of chemicals as a high-content screening tool.
Ključne besede: in vitro 3D cell model, HepG2, flow cytometry, cell cycle, proliferation, DNA strand, breaks
Objavljeno v DiRROS: 16.07.2024; Ogledov: 26; Prenosov: 20
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3. Combined toxic effects of BPA and its two analogues BPAP and BPC in a 3D HepG2 cell modelMartina Štampar, Tim Ravnjak, Ana-Marija Domijan, Bojana Žegura, 2023, izvirni znanstveni članek Povzetek: Bisphenol A (BPA) is one of the most commonly used substances in the manufacture ofvarious everyday products. Growing concerns about its hazardous properties, including endocrinedisruption and genotoxicity, have led to its gradual replacement by presumably safer analogues inmanufacturing plastics. The widespread use of BPA and, more recently, its analogues has increasedtheir residues in the environment. However, our knowledge of their toxicological profiles is limitedand their combined effects are unknown. In the present study, we investigated the toxic effectscaused by single bisphenols and by the combined exposure of BPA and its two analogues, BPAP andBPC, after short (24-h) and prolonged (96-h) exposure in HepG2 spheroids. The results showed thatBPA did not reduce cell viability in HepG2 spheroids after 24-h exposure. In contrast, BPAP andBPC affected cell viability in HepG2 spheroids. Both binary mixtures (BPA/BPAP and BPA/BPC)decreased cell viability in a dose-dependent manner, but the significant difference was only observedfor the combination of BPA/BPC (both at 40μM). After 96-h exposure, none of the BPs studiedaffected cell viability in HepG2 spheroids. Only the combination of BPA/BPAP decreased cellviability in a dose-dependent manner that was significant for the combination of 4μM BPA and 4μMBPAP. None of the BPs and their binary mixtures studied affected the surface area and growth ofspheroids as measured by planimetry. In addition, all BPs and their binary mixtures studied triggeredoxidative stress, as measured by the production of reactive oxygen species and malondialdehyde,at both exposure times. Overall, the results suggest that it is important to study the effects of BPsas single compounds. It is even more important to study the effects of combined exposures, as thecombined effects may differ from those induced by single compounds.
Ključne besede: BP analogues, hepatic in vitro 3D cell model, combined exposure, viability, oxidative stress, toxicology
Objavljeno v DiRROS: 12.07.2024; Ogledov: 40; Prenosov: 17
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4. Adverse (geno)toxic effects of bisphenol A and its analogues in hepatic 3D cell modelMarta Sendra, Martina Štampar, Katarina Fras, Beatriz Novoa, Antonio Figueras, Bojana Žegura, 2023, izvirni znanstveni članek Ključne besede: BPA analogues, in vitro 3D cell model, genotoxic, DNA strand breaks, cell proliferation, cell death
Objavljeno v DiRROS: 12.07.2024; Ogledov: 47; Prenosov: 21
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5. Uporabnost nacionalnih podatkov laserskega skeniranja in cikličnega aerofotografiranja pri zaznavanju gozdnih vrzeliAnže Martin Pintar, Mitja Skudnik, 2024, izvirni znanstveni članek Povzetek: Gozdna tla zastirajo drevesne krošnje in gozdna vrzel je vsaka večja ali manjša površina tal, ki je ne prekrivajo krošnje zgornjega sloja dreves. Velikost vrzeli vpliva na to, katera drevesna vrsta se bo pomladila, pa tudi na vertikalno in horizontalno strukturo gozda. Na Pohorju (Pahernikova gozdna posest, za katero so značilni gozdovi, v katerih se na majhnih površinah pojavljajo drevesa različnih premerov in starosti) smo analizirali možnosti samodejnega zaznavanja vrzeli na podlagi podatkov Laserskega skeniranja Slovenije (LSS) in Cikličnega aerofotografiranja Slovenije (CAS). Uporabili smo digitalna modela krošenj (DMK), pridobljena iz obeh virov podatkov. Skupna natančnost zaznavanja tudi najmanjših vrzeli (manjših od 50 m2 ) na podlagi podatkov LSS je znašala 94,4 %, na podlagi podatkov CAS pa 83,1 %. Na podlagi podatkov LSS je mogoče zaznati večje število in površino vrzeli, prav tako so vrzeli, pridobljene na podlagi podatkov LSS, bolj razčlenjene in podolgovate. Zaznavanje vrzeli s podatki CAS in LSS je medsebojno bolj primerljivo pri najmanjših površinah vrzeli 100 m2 , natančnost zaznave takšnih vrzeli je 85,4 oziroma 94,4 %. Rezultati kažejo, da je ob odsotnosti podatkov LSS uporaba podatkov CAS za določanje vrzeli smiselna na velikopovršinski ravni in pri zaznavanju vrzeli, večjih od 100 m2 .
Ključne besede: raznomerni gozdovi, raznodobni gozdovi, digitalni model krošenj, gozdna vrzel, daljinsko zaznavanje, Lasersko skeniranje Slovenije, LSS, Ciklično aerofotografiranje Slovenije, CAS
Objavljeno v DiRROS: 08.07.2024; Ogledov: 69; Prenosov: 25
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6. 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: 115; Prenosov: 98
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7. 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: 169; Prenosov: 122
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8. Discovering unknown Madagascar biodiversity : integrative taxonomy of raft spiders (Pisauridae: Dolomedes)Kuang-Ping Yu, Matjaž Kuntner, 2024, izvirni znanstveni članek Povzetek: Madagascar is a global biodiversity hotspot, but its biodiversity continues to be underestimated and understudied. Of raft spiders, genus Dolomedes Latreille, 1804, literature only reports two species on Madagascar. Our single expedition to humid forests of eastern and northern Madagascar, however, yielded a series of Dolomedes exemplars representing both sexes of five morphospecies. To avoid only using morphological diagnostics, we devised and tested an integrative taxonomic model for Dolomedes based on the unified species concept. The model first determines morphospecies within a morphometrics framework, then tests their validity via species delimitation using COI. It then incorporates habitat preferences, geological barriers, and dispersal related traits to form hypotheses about gene flow limitations. Our results reveal four new Dolomedes species that we describe from both sexes as Dolomedes gregoric sp. nov., D. bedjanic sp. nov., D. hydatostella sp. nov., and D. rotundus sp. nov. The range of D. kalanoro Silva & Griswold, 2013, now also known from both sexes, is expanded to eastern Madagascar. By increasing the known raft spider diversity from one valid species to five, our results merely scratch the surface of the true Dolomedes species diversity on Madagascar. Our integrative taxonomic model provides the framework for future revisions of raft spiders anywhere.
Ključne besede: raft spiders, integrative taxonomic model, Madagascar, biodiversity, integrative taxonomy, zoology
Objavljeno v DiRROS: 16.05.2024; Ogledov: 227; Prenosov: 261
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9. Verjetnostna napoved sanitarnega poseka smreke zaradi podlubnikov v Sloveniji v 2024Nikica Ogris, Maarten De Groot, 2024, drugi znanstveni članki Ključne besede: gozdovi, varstvo gozdov, navadna smreka, Picea abies, sanitarni posek, napoved, prognoza, ogroženost, model, smrekovi podlubniki, Ips typographus, Pityogenes chalcographus
Objavljeno v DiRROS: 19.04.2024; Ogledov: 260; Prenosov: 112
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