1. Crayfish pet trade as a pathway for the introduction of known and novel virusesKatarina Bačnik, Luka Kranjc, Leticia Botella, Ivana Maguire, Dora Pavić, Jiří Patoka, Paula Dragičević, Martin Blaha, Ana Bielen, Antonín Kouba, Denis Kutnjak, Sandra Hudina, 2025, izvirni znanstveni članek Povzetek: Expanding international pet trade has emerged as one of the main introduction pathways of aquatic invasive species, with ornamental crayfish species commonly available on the EU and global markets. Besides most frequently studied crayfish pathogens, such as Aphanomyces astaci and white spot syndrome virus (WSSV), ornamental crayfish carry associated microbial communities, which may potentially lead to the emergence of known or even novel diseases following intentional or unintentional release of animals into the wild. This is especially problematic in the case of viruses, which represent an important, yet considerably understudied, group of crayfish pathogens. Here we analyzed viromes of hepatopancreas tissue of four crayfish species acquired in the international pet trade in Europe (Procambarus clarkii, Procambarus alleni, Cherax holthuisi, and Cherax quadricarinatus) using a high throughput sequencing based metagenomic approach. Seven different known viruses were identified, which were previously either directly associated with crayfish (WSSV, Cherax quadricarinatus reovirus, chequa iflavirus, athtab bunya-like virus) or with hosts from subphylum Crustacea or invertebrates associated with freshwater environment (Shahe ispoda virus 5, Dicistroviridae sp.). Additional sequences represented 8 potential novel and divergent RNA viruses, most similar to sequences belonging to members of Picornavirales, Elliovirales, Reovirales, Hepelivirales, Tolivirales and Ghabrivirales orders. We discuss our findings in relation to their phylogenetic relationships, geographical origins, and putative pathogenicity implications. The results highlight the need for further research into the risks related to disease emergence associated with the pet trade.
Ključne besede: virome, RNA viruses, ornamental crayfish, pet-trade, high throughput sequencing, ecology, molecular biology, pathology, virology, environmental risk assessment
Objavljeno v DiRROS: 23.05.2025; Ogledov: 637; Prenosov: 421
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2. Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastlineNataša Mehle, Denis Kutnjak, Ana Vučurović, Ion Gutiérrez-Aguirre, Katarina Bačnik, Luka Kranjc, Irena Bajde, Jakob Brodarič, Maja Ravnikar, Olivera Maksimović, Mark Paul Selda Rivarez, Tomaž Curk, Neža Pajek Arambašić, Rok Štravs, 2024, končno poročilo o rezultatih raziskav Ključne besede: diagnostika, rastlinski virusi, ToBRFV, ToMMV, tobamovirusi, epidemiologija, voda kot vir okužb, poročila
Objavljeno v DiRROS: 20.02.2025; Ogledov: 655; Prenosov: 210
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3. Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastline : aplikativni raziskovalni projekt L4-3179Nataša Mehle, Denis Kutnjak, Tomaž Curk, Neža Pajek Arambašić, Ion Gutiérrez-Aguirre, Rok Štravs, Katarina Bačnik, Luka Kranjc, Irena Bajde, Jakob Brodarič, Miha Kitek, Maja Ravnikar, Olivera Maksimović, Mark Paul Selda Rivarez, Ana Vučurović, 2024, končno poročilo o rezultatih raziskav Ključne besede: ToBRFV, ToMMV, tobamovirusi, epidemiologija, voda kot vir okužb, poročila
Objavljeno v DiRROS: 28.11.2024; Ogledov: 862; Prenosov: 715
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4. Identification of triazolopyrimidinyl scaffold SARS-CoV-2 papain-like protease (PLpro) inhibitorSebastjan Kralj, Marko Jukič, Miha Bahun, Luka Kranjc, Anja Kolarič, Milan Hodošček, Nataša Poklar Ulrih, Urban Bren, 2024, izvirni znanstveni članek Povzetek: The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PLpro), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PLpro, with an IC50 value of 82 ± 34 μM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PLpro, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PLpro inhibitor development, this study elaborates on the PLpro binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PLpro inhibitor development.
Ključne besede: drug design, protease inhibitor, SARS-CoV-2, papain-like protease, PLpro, antiviral design, in silico drug design, CADD, virtual screening, HTVS, structure-based design
Objavljeno v DiRROS: 07.08.2024; Ogledov: 863; Prenosov: 716
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5. Simple and reliable in situ CRISPR-Cas9 nuclease visualization tool is ensuring efficient editing in Streptomyces speciesAlen Pšeničnik, Roman Reberšek, Lucija Slemc, Tim Godec, Luka Kranjc, Hrvoje Petković, 2022, izvirni znanstveni članek Povzetek: CRISPR-Cas9 technology has emerged as a promising tool for genetic engineering of Streptomyces strains. However, in practice, numerous technical hurdles have yet to be overcome when developing robust editing procedures. Here, we developed an extension of the CRISPR-Cas toolbox, a simple and reliable cas9 monitoring tool with transcriptional fusion of cas9 nuclease to a beta glucuronidase (gusA) visual reporter gene. The Cas9-SD-GusA tool enables in situ identification of cells expressing Cas9 nuclease following the introduction of the plasmid carrying the CRISPR-Cas9 machinery. Remarkably, when the Cas9-SD-GusA system was applied under optimal conditions, 100% of the colonies displaying GusA activity carried the target genotype. In contrast, it was shown that the cas9 sequence had undergone major recombination events in the colonies that did not exhibit GusA activity, giving rise to “escaper colonies” carrying unedited genotype. Our approach allows a simple detection of “escaper” phenotype and serves as an efficient CRISPR-Cas9 optimisation tool.
Ključne besede: CRISPR-Cas9, gusA visual screening, "CRISPR escaper colonies", Streptomyces
Objavljeno v DiRROS: 17.07.2024; Ogledov: 750; Prenosov: 549
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6. Microstructure and properties variation of high-performance grey cast iron via small boron additionsGrega Klančnik, Jaka Burja, Urška Klančnik, Barbara Šetina, Luka Krajnc, Andrej Resnik, 2024, izvirni znanstveni članek Ključne besede: boron, cast iron, solidification, thermal analysis, Thermo-Calc
Objavljeno v DiRROS: 07.02.2024; Ogledov: 1124; Prenosov: 681
Celotno besedilo (3,11 MB)
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