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232. Poročilo o preskusu št.: LVG 2024-153 : vzorec št. 2024/00608Barbara Piškur, Zina Devetak, Patricija Podkrajšek, Špela Hočevar, Nikica Ogris, 2024, expertise, arbitration decision Keywords: varstvo gozdov, morfološke analize, Pseudocercospora pini-densiflorae, rdeči bor, bolezen iglic
Published in DiRROS: 23.10.2024; Views: 55; Downloads: 0
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233. Knots and $\theta$-curves identification in polymeric chains and native proteins using neural networksFernando Bruno da Silva, Boštjan Gabrovšek, Marta Korpacz, Kamil Luczkiewicz, Szymon Niewieczerzal, Maciej Sikora, Joanna I. Sulkowska, 2024, original scientific article Abstract: Entanglement in proteins is a fascinating structural motif that is neither easy to detect via traditional methods nor fully understood. Recent advancements in AI-driven models have predicted that millions of proteins could potentially have a nontrivial topology. Herein, we have shown that long short-term memory (LSTM)-based neural networks (NN) architecture can be applied to detect, classify, and predict entanglement not only in closed polymeric chains but also in polymers and protein-like structures with open knots, actual protein configurations, and also $\theta$-curves motifs. The analysis revealed that the LSTM model can predict classes (up to the $6_1$ knot) accurately for closed knots and open polymeric chains, resembling real proteins. In the case of open knots formed by protein-like structures, the model displays robust prediction capabilities with an accuracy of 99%. Moreover, the LSTM model with proper features, tested on hundreds of thousands of knotted and unknotted protein structures with different architectures predicted by AlphaFold 2, can distinguish between the trivial and nontrivial topology of the native state of the protein with an accuracy of 93%.
Keywords: machine learning, topology, protein databases, entanglements, open knots, closed knots
Published in DiRROS: 23.10.2024; Views: 76; Downloads: 32
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234. Kakovost peletov na slovenskem trgu v letu 2024Darja Stare, Peter Prislan, Matjaž Dremelj, Amina Gačo, 2023, treatise, preliminary study, study Keywords: gozdarstvo, lesna biomasa, trg lesnih goriv, peleti, kakovost
Published in DiRROS: 23.10.2024; Views: 59; Downloads: 30
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235. Poročilo o preskusu št.: LVG 2024-152 : vzorec št. 2024/00809Nikica Ogris, Patricija Podkrajšek, Špela Hočevar, Barbara Piškur, 2024, expertise, arbitration decision Keywords: varstvo gozdov, morfološke analize, program preiskav, Fusarium circinatum, borov smolasti rak, PCR v realnem času
Published in DiRROS: 23.10.2024; Views: 47; Downloads: 2
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236. Discovery of novel and known viruses associated with toxigenic and non-toxigenic bloom forming diatoms from the Northern Adriatic SeaTimotej Turk Dermastia, Denis Kutnjak, Ion Gutiérrez-Aguirre, Corina P. D. Brussaard, Katarina Bačnik, 2024, original scientific article Abstract: Algal blooms impact trophic interactions, community structure and element fluxes. Despite playing an important role in the demise of phytoplankton blooms, only few viruses infecting diatoms have been cultured. Pseudo-nitzschia is a widespread diatom genus that commonly blooms in coastal waters and contains toxin-producing species. This study describes the characterization of a novel virus infecting the toxigenic species Pseudo-nitzschia galaxiae isolated from the northern Adriatic Sea. The ssRNA virus PnGalRNAV has 29.5 nm ± 1.2 nm icosahedral virions and a genome size of 8.8 kb. It belongs to the picorna-like Marnaviridae family and shows high specificity for P. galaxiae infecting two genetically and morphologically distinct strains. We found two genetically distinct types of this virus and screening of the global virome database revealed matching sequences from the Mediterranean region and China, suggesting its global distribution. Another virus of similar shape and size infecting Pseudo-nitzschia calliantha was found, but its genome could not be determined. In addition, we have obtained and characterized a new virus that infects Chaetoceros tenuissimus. The replicase protein of this virus is very similar to the previously described ChTenDNAV type-II virus, but it has a unique genome and infection pattern. Our study is an important contribution to the collective diatom virus culture collection and will allow further investigation into how these viruses control diatom bloom termination, carbon export and toxin release in the case of Pseudo-nitzschia.
Keywords: algal blooms, diatoms, virus, PnGalRNAV, genome, Adriatic Sea, marine virology, phytoplankton ecology, marine biology
Published in DiRROS: 23.10.2024; Views: 55; Downloads: 26
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240. Differences in distribution and characteristics of microplastics in sediments of the south-eastern part of the Gulf of TriesteJena Jamšek, Helena Prosen, Oliver Bajt, 2024, original scientific article Abstract: Introduction: The Gulf of Trieste is prone to the accumulation of various pollutants and microplastics due to its geomorphological and hydrological characteristics. However, the distribution and sources of microplastics in this semi-enclosed area are poorly studied. The aim of our study was to determine the distribution and chemical composition of MP particles in the sediments of the Gulf of Trieste. Methods: In this study, we collected 24 surface sediment samples using a Van Veen grab. Microplastics were extracted by density separation using NaCl. The size, shape, and color of the extracted microplastics were determined using an optical microscope, and the composition of the polymers was determined by Fourier transform infrared spectroscopy. Results and discussion: The highest concentrations of up to 125 microplastic particles per 100 g dry sediment were found in coastal areas. Concentrations in the open sea were much lower, with an average of 3 particles per 100 g of sediment. Most of the microplastic was fibrous, made of polypropylene, 100–300 µm in size, and blue. This is the first study showing that microplastics are present in the sediments of the south-eastern part of the Gulf of Trieste. The findings suggest that microplastics exhibit a tendency to be retained within the sediment, leading to their accumulation primarily in a narrow coastal area rather than dispersing offshore. Our results will contribute to a better knowledge of the distribution and possible sources of plastics and microplastics in the Gulf of Trieste and even beyond in similar semi-enclosed marine areas.
Keywords: microplastics, sediments, Gulf of Trieste, density separation, polypropylene, accumulation of pollutants, marine biology
Published in DiRROS: 23.10.2024; Views: 51; Downloads: 27
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