1. A new locality for the blind loach, Eidinemacheilus smithi (Teleostei: Nemacheilidae) in Iranian Zagros : a morpho-molecular approachMohammad Javad Malek-Hosseini, Yaser Fatemi, Hamid Reza Esmaeili, Tjaša Lokovšek, Matjaž Kuntner, 2022, izvirni znanstveni članek Povzetek: Four obligate cave fish species have been recorded from Zagros in Iran: Garra typhlops (Bruun and Kaiser, 1944), G. lorestanensis (Mousavi-Sabet and Eagderi, 2016), G. tashanensis (Mousavi-Sabet, Vatandoust, Fatemi and Eagderi, 2016) and Eidinemacheilus smithi (Greenwood, 1976). So far, the only known locality of the latter has been the Loven cave. Here, we extend the known range of the Zagros blind loach (E. smithi) by reporting a new locality, the Tuveh spring, located 31 km south of Loven. We combine morphological evidence with the calculated K2P genetic divergences of 1.39% between Tuveh and Loven to confirm that these populations are conspecific. Our discovery of the second E. smithi population has implications for the conservation of this rare and vulnerable species.
Ključne besede: fishes, caves, evolution, Irano-Anatolian hotspot
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2. Poročilo o preskusu št.: LVG 2024-067 : vzorec št. 2024/00318Nikica Ogris, Špela Hočevar, Zina Devetak, Barbara Piškur, 2024, izvedensko mnenje, arbitražna odločba Ključne besede: varstvo gozdov, morfološke analize, program preiskav, Fusarium circinatum, Pinus, borov smolasti rak, PCR
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5. Controlling gene expression with deep generative design of regulatory DNAJan Zrimec, Xiaozhi Fu, Azam Sheikh Muhammad, Christos Skrekas, Vykintas Jauniskis, Nora K. Speicher, Christoph S. Börlin, Vilhelm Verendel, Morteza Haghir Chehreghani, Devdatt P. Dubhashi, Verena Siewers, Florian David Fitz, Jens Nielsen, Aleksej Zelezniak, 2022, izvirni znanstveni članek Povzetek: Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Using mutagenesis typically requires screening sizable random DNA libraries, which limits the designs to span merely a short section of the promoter and restricts their control of gene expression. Here, we prototype a deep learning strategy based on generative adversarial networks (GAN) by learning directly from genomic and transcriptomic data. Our ExpressionGAN can traverse the entire regulatory sequence-expression landscape in a gene-specific manner, generating regulatory DNA with prespecified target mRNA levels spanning the whole gene regulatory structure including coding and adjacent non-coding regions. Despite high sequence divergence from natural DNA, in vivo measurements show that 57% of the highly-expressed synthetic sequences surpass the expression levels of highly-expressed natural controls. This demonstrates the applicability and relevance of deep generative design to expand our knowledge and control of gene expression regulation in any desired organism, condition or tissue.
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6. Diversity of molluscan assemblage in relation to biotic and abiotic variables in brown algal forestsMartina Orlando-Bonaca, Domen Trkov, Katja Klun, Valentina Pitacco, 2022, izvirni znanstveni članek Povzetek: Canopy-forming macroalgae, mainly those belonging to the order Fucales, form the so-called brown algal forests, which are among the most productive assemblages in shallow coastal zones. Their vertical, branching canopies increase nearshore primary production, provide nursery areas for juvenile fish, and sustain understory assemblages of smaller algae and both sessile and vagile fauna. The majority of benthic invertebrates inhabiting these forests have larval stages that spend some time floating freely or swimming in the plankton. Therefore, canopy-forming macroalgae play an important role as species collectors related to larval supply and hydrodynamic processes. During the past several decades, brown algal forests have significantly reduced their extension and coverage in the Mediterranean basin, due to multiple interacting natural and anthropogenic pressures, with negative consequences also for the related fauna. The aim of this research was to examine how differences in macrophyte abundance and structure, as well as environmental variables, affect the associated molluscan communities in the shallow northern Adriatic Sea. Sampling sites with well-developed vegetation cover dominated by different canopy-forming species were selected in the shallow infralittoral belt of the northern Adriatic Sea in the spring–summer period of the years 2019 and 2020. Our results confirm the importance of algal forests for molluscan assemblage, with a total of 68 taxa of molluscs found associated with macrophytes. Gastropods showed the highest richness and abundance, followed by bivalves. Mollusc richness and diversity (in terms of biotic indices) were not related with the degree of development of canopy-forming species (in terms of total cover and total volume), nor with the ecological status of benthic macroalgae at different depths. On the contrary, the variability in molluscan taxa abundances was explained by some environmental variables, such as temperature, pH, light, and nitrates concentration.
Ključne besede: canopy-forming algae, coverage, molluscan assemblage, diversity, abiotic factors, Adriatic Sea
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8. An insight into the feeding ecology of Serranus Scriba, a Shallow water mesopredator in the Northern Adriatic Sea, with a non-destructive methodAna Lokovšek, Martina Orlando-Bonaca, Domen Trkov, Lovrenc Lipej, 2022, izvirni znanstveni članek Povzetek: Serranus scriba is a common member of the coastal fish community in the Adriatic Sea, but knowledge about its feeding ecology is scarce. The aim of this paper is to present new evidence about its food preferences and feeding habits. An innovative non-destructive method of fecal pellet analysis was used for this study. This method does not require sacrificing specimens and the fish can be released back into the sea alive after the laboratory work. The results demonstrated that S. scriba mainly preys on decapods, followed by polychaetes, isopods, fish, mollusks and swarming shrimps. The calculated index of trophic diversity (ITD) value of 0.89 indicates that it is an opportunistic feeder that feeds on a wide range of different prey. According to the calculated trophic level of 3.43, which is higher than that of other members of the community, S. scriba is also an important piscivorous predator. With age, S. scriba undergoes an ontogenetic shift. The proportion of crustaceans, gastropods and polychaetes decreases with age and body size, while the proportion of fish increases.
Ključne besede: coastal fishes, diet, non-destructive method, non-lethal method, painted comber, northern Adriatic
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9. Evaluation of methods and processes for robust monitoring of SARS-CoV-2 in wastewaterOlivera Maksimović, Živa Lengar, Zala Kogej Zwitter, Katarina Bačnik, Irena Bajde, Mojca Milavec, Anže Županič, Nataša Mehle, Denis Kutnjak, Maja Ravnikar, Ion Gutiérrez-Aguirre, 2022, izvirni znanstveni članek Povzetek: The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
Ključne besede: waste water, method evolution, virus detection, SARS-CoV-2
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10. What did we achieve with VALITEST an EU project on validation in plant pest diagnostics?Charlotte Trontin, Barbara Agstner, Denise Altenbach, Géraldine Anthoine, Hanna Baginska, Ian Brittain, A Chabirand, Anne-Marie Chappé, P. Dahlin, Tanja Dreo, C. Freye-Minks, Camilo Gianinazzi, Catherine Harrison, Glyn Jones, Marco Stefan Kaiser, Marta Luigi, Sébastien Massart, Nataša Mehle, Monica Mezzalama, Hanna Mouaziz, Maja Ravnikar, Tom Raaymakers, Jean-Philippe Renvoise, Mathieu Rolland, Marta Santos, Sam Seddas, René van der Vlugt, Ana Vučurović, Françoise Petter, 2022, izvirni znanstveni članek Ključne besede: plant pest diagnostics, validation, test performance study, high-throughput, sequencing, reference material, training
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