611. Challenges in harmonized assessment of heavy metals in the Adriatic and Ionian SeasDaniela Berto, Margherita Malgorzata Formalewicz, Giordano Giorgi, Federico Rampazzo, Claudia Gion, Benedetta Trabucco, Michele Giani, Marina Lipizer, Slavica Matijević, Helen Kaberi, Christina Zeri, Oliver Bajt, Nevenka Mikac, Danijela Joksimović, Andriana Aravantinou, Mateja Poje, Magdalena Cara, Loredana Manfra, 2020, original scientific article Abstract: The Adriatic-Ionian region (ADRION Region) shows strong development in terms of urban expansion in coastal and inland areas as well as increasing maritime traffic and offshore hydrocarbon extraction activities. A serious risk of pollution arises from hazardous substances requiring reliable and coherent monitoring and assessment programs. EU Directives (WFD – Water Framework Directive, MSFD – Marine Strategy Framework Directive) and Barcelona Convention protocols, aim to assess the level of pollution with the objective to implement measures to prevent and/or mitigate impacts on the marine environment. This high level integration process has to be based on common and agreed protocols for monitoring of contaminants. Aiming to share best practices to encourage a harmonized implementation of monitoring and assessment of contaminants, an extensive review of monitoring and analytical protocols adopted by six EU and non-EU countries along the Adriatic and Ionian seas was carried out in the framework of the Interreg Adrion project HarmoNIA (Interreg V-B Adriatic-Ionian (ADRION), 2018–2020). This paper presents a methodological proposal to define a common protocol for the evaluation of the metal contamination of seawater, sediment and biota. Contaminants have been chosen following preliminary consultations among countries of the ADRION area, considering objectives of WFD and MSFD, as well as Environmental Impact Assessment (EIA) procedures for offshore platforms. Information was gathered relative to matrix characteristics and quality assurance/quality control of the analytical performance (sample preservation, analytical methodology, reference materials, limit of detection, and limit of quantification, accuracy, reproducibility, etc.). The comparison of information provided by laboratories of nine institutions highlighted the request for harmonization in terms of sampling procedures, matrix characterization, preservation procedures, analytical methods and LOQ values. Although appropriate environmental quality standards for biota and sediment matrices should be established at national level and also through regional and sub-regional cooperation, as required by the WFD and MSFD, the proposed LOQ values, even if challenging, represent a benchmark and a stimulus to optimize analytical performance, to ensure the best level of protection to the coastal and offshore environment in the ADRION Region. Keywords: hazardous substances, harmonized protocols, integrated approach, monitoring, assessment of contaminants, heavy metals, Adriatic-Ionian Sea region Published in DiRROS: 22.07.2024; Views: 242; Downloads: 154
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612. Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potatoMarko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Špela Tomaž, Elizabeth Tseng, Mohamed Zouine, Anna Coll Rius, Kristina Gruden, 2020, original scientific article Abstract: Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes. Published in DiRROS: 22.07.2024; Views: 168; Downloads: 125
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613. Challenges in harmonized environmental impact assessment (EIA), monitoring and decommissioning procedures of offshore platforms in Adriatic-Ionian (ADRION) regionLoredana Manfra, Claudia Virno Lamberti, Silvia Ceracchi, Giordano Giorgi, Daniela Berto, Marina Lipizer, Michele Giani, Oliver Bajt, Maja Fafanđel, Magdalena Cara, Slavica Matijević, Milena Mitrić, Stefanos Papazisimou, Mateja Poje, Christina Zeri, Benedetta Trabucco, 2020, original scientific article Abstract: A harmonized and integrated approach for monitoring and assessment of contamination, including hydrocarbon exploitation one, is required both by Marine Strategy Framework Directive (MSFD) at EU level and by the Ecosystem Approach (EcAp) program of the Barcelona Convention at Mediterranean level. A broad review of protocols of environmental impact assessment (EIA) procedures, monitoring and decommissioning of offshore platforms adopted by EU and non-EU countries along the Adriatic-Ionian seas was carried out in the framework of the Interreg offshore platforms in Adriatic-Ionian (ADRION) project HarmoNIA (Harmonization and networking for contaminant assessment in the Ionian and Adriatic Seas). The comparison of information provided by six ADRION countries and the application of a harmonized and integrated approach has highlighted specific challenges for managing offshore platform impacts emerged at ADRION level: (i) need of the same legislative level (the Offshore Protocol of Barcelona Convention is not ratified by all countries); (ii) set up of a task force of ADRION experts for discussing critical issues related to impacts of offshore platforms; (iii) harmonization, at the regional level, of EIA procedures, monitoring and decommissioning; (iv) need of an agreed and common list of recommended parameters to monitor in water, sediment and biota for the assessment of impacts due to platform installations and PFW discharges. Keywords: harmonized protocols, environmental impact assessment, monitoring, decommissioning, offshore platforms, Adriatic-Ionian Sea region, MSFD, Barcelona Convention Published in DiRROS: 22.07.2024; Views: 274; Downloads: 93
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614. Precision transcriptomics of viral foci reveals the spatial regulation of immune-signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potatoTjaša Lukan, Maruša Pompe Novak, Špela Baebler, Magda Tušek-Žnidarič, Aleš Kladnik, Maja Križnik, Andrej Blejec, Maja Zagorščak, Katja Stare, Barbara Dušak, Anna Coll Rius, Stephan Pollmann, Karolina Morgiewicz, Jacek Hennig, Kristina Gruden, 2020, original scientific article Abstract: Whereas the activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to the restriction of the pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels in order to reveal the spatiotemporal regulation of the immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA-deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed and the spread of the virus is not arrested at the site of infection. RBOHD is required for the spatial accumulation of SA, and conversely RBOHD is under the transcriptional regulation of SA. Using spatially resolved RNA-seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling. Keywords: immune signaling network, NADPH oxidase RBOHD, reactive oxygen species, salicylic acid, Sola-num tuberosum (potato), spatiotemporal response analysis, virus resistance, Potyvirus Published in DiRROS: 22.07.2024; Views: 159; Downloads: 125
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615. Machine learning approaches identify male body size as the most accurate predictor of species richnessKlemen Čandek, Urška Pristovšek, Matjaž Kuntner, 2020, original scientific article Abstract: Background
A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness –the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera.
Results
We test the predictive power of 22 variables from spiders’ morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness.
Conclusions
We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly. Keywords: biodiversity, lineage diversity, species traits, spiders, phylogenetic diversity, species distribution, random forest, multiple correspondence analysis Published in DiRROS: 22.07.2024; Views: 284; Downloads: 260
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616. Lagrangian modelling of a person lost at sea during the Adriatic scirocco storm of 29 October 2018Matjaž Ličer, Solène Estival, Catalina Reyes-Suarez, Davide Deponte, Anja Fettich, 2020, original scientific article Abstract: On 29 October 2018 a windsurfer's mast broke about 1 km offshore from Istria during a severe scirocco storm in the northern Adriatic Sea. He drifted in severe marine conditions until he eventually beached alive and well in Sistiana (Italy) 24 h later. We conducted an interview with the survivor to reconstruct his trajectory and to gain insight into his swimming and paddling strategy. Part of survivor's trajectory was verified using high-frequency radar surface current observations as inputs for Lagrangian temporal back-propagation from the beaching site. Back-propagation simulations were found to be largely consistent with the survivor's reconstruction. We then attempted a Lagrangian forward-propagation simulation of his trajectory by performing a leeway simulation using the OpenDrift tracking code using two object types: (i) person in water in unknown state and (ii) person with a surfboard. In both cases a high-resolution (1 km) setup of the NEMO v3.6 circulation model was employed for the surface current component, and a 4.4 km operational setup of the ALADIN atmospheric model was used for wind forcing. The best performance is obtained using the person-with-a-surfboard object type, giving the highest percentage of particles stranded within 5 km of the beaching site. Accumulation of particles stranded within 5 km of the beaching site saturates 6 h after the actual beaching time for all drifting-particle types. This time lag most likely occurs due to poor NEMO model representation of surface currents, especially in the final hours of the drift. A control run of wind-only forcing shows the poorest performance of all simulations. This indicates the importance of topographically constrained ocean currents in semi-enclosed basins even in seemingly wind-dominated situations for determining the trajectory of a person lost at sea. Published in DiRROS: 22.07.2024; Views: 163; Downloads: 105
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617. 2D and 3D in vitro assays to quantify the invasive behavior of glioblastoma stem cells in response to SDF-1[alpha]Vashendriya V. V. Hira, Barbara Breznik, Cornelis J. F. van Noorden, Tamara Lah Turnšek, Remco J. Molenaar, 2020, original scientific article Abstract: Invasion is a hallmark of cancer and therefore in vitro invasion assays are important tools in cancer research. We aimed to describe in vitro 2D transwell assays and 3D spheroid assays to quantitatively determine the invasive behavior of glioblastoma stem cells in response to the chemoattractant SDF-1α. Matrigel was used as a matrix in both assays. We demonstrated quantitatively that SDF-1α increased invasive behavior of glioblastoma stem cells in both assays. We conclude that the 2D transwell invasion assay is easy to perform, fast and less complex whereas the more time-consuming 3D spheroid invasion assay is physiologically closer to the in vivo situation. Keywords: 2D transwell invasion assay, 3D spheroid invasion assay, cancer cell, cellular invasion, glioblastoma stem cells Published in DiRROS: 22.07.2024; Views: 154; Downloads: 144
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618. The effect of three polyphenols and some other anti-oxidant substances on amyloid fibril formation by human cystatin CAlma Jahić, Magda Tušek-Žnidarič, Sara Pintar, Selma Berbić, Eva Žerovnik, 2020, original scientific article Abstract: Human cystatin C (CysC) is an amyloid forming protein involved in the hereditary cerebral amyloid angiopathy (HCCAA) that affects arteries in the brain and the peripheral nervous system. In this study we measured the influence of several substances on human CysC aggregation and amyloid fibril formation, induced at pH 4 in vitro. The effect of three polyphenols: resveratrol, quercetin and curcumin and of two antioxidants: vitamin C (VitC) and N-acetyl-L-cysteine (NAC) was explored as well as the effect of sulphoraphane (SF) and α-lipoic acid (AL). The formation of amyloid fibrils was followed by Thioflavin T (ThT) fluorescence and by transmission electron microscopy (TEM). Effects on the length of the lag phase were revealed by following the increase of ThT fluorescence intensity with time. The amount and morphology of fibrils in comparison to prefibrillar aggregates and globular oligomers were evaluated by TEM at the plateau stage of the reaction. Thermal stabilization of the CysC monomer by the small compounds was measured by differential scanning fluorimetry (DSF). NAC, VitC and SF exhibited the largest inhibitory effect on amyloid fibril growth. The effects of polyphenols were not significant, apart from resveratrol, which partly inhibited the amyloid fibril growth. Published in DiRROS: 22.07.2024; Views: 166; Downloads: 98
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619. Validating the potential of double-stranded RNA targeting Colorado potato beetle mesh gene in laboratory and field trialsMarko Petek, Anna Coll Rius, Rok Ferenc, Jaka Razinger, Kristina Gruden, 2020, original scientific article Abstract: Colorado potato beetle (CPB) is an agricultural pest of solanaceous crops, notorious for its rapid resistance development to chemical pesticides. Foliar spraying of dsRNA formulations is a promising innovative technology providing highly specific and environmentally acceptable option for CPB management. We designed dsRNA to silence CPB mesh gene (dsMESH) and performed laboratory feeding trials to assess impacts on beetle survival and development. We compared the effectiveness of in vivo and in vitro produced dsRNA in a series of laboratory experiments. We additionally performed a field trial in which the efficacy of dsRNA sprayed onto potato foliage was compared to a spinosad-based insecticide. We showed that dsMESH ingestion consistently and significantly impaired larval growth and decreased larval survival in laboratory feeding experiments. In vivo produced dsRNA performed similarly as in vitro synthesized dsRNA in laboratory settings. In the field trial, dsMESH was as effective in controlling CPB larvae as a commercial spinosad insecticide, its activity was however slower. We discuss limitations and benefits of a potential dsMESH-based CPB management strategy and list some important RNAi based CPB research topics, which will have to be addressed in future. Keywords: RNA interference, RNA interference feeding, ds RNA, gene silencing, RNAi pest control, survival analysis, field trial Published in DiRROS: 22.07.2024; Views: 159; Downloads: 57
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620. Development and validation of a new TaqMan real-time PCR for detection of 'Candidatus phytoplasma pruni'Zala Kogej Zwitter, Marina Dermastia, Nataša Mehle, 2020, original scientific article Abstract: Phytoplasmas of the 16SrIII group are wide spread, and have a broad plant host range. Among these, ‘Candidatus phytoplasma pruni’ (‘Ca. P. pruni’; phytoplasmas of 16SrIII subgroup A) can cause serious diseases in Prunus species and ‘Ca. P. pruni’-related strains can infect other plant species, including grapevines. In this study, a new real-time PCR detection system was developed for ‘Ca. P. pruni’ using TaqMan chemistry. This test was designed to detect ‘Ca. P. pruni’, by amplifying the species-specific secY gene. In addition, a test to amplify the group-specific 16S rRNA gene region was also developed. The performances of both tests were evaluated. The test that amplifies the secY gene provided reliable and quick detection of ‘Ca. P. pruni’. Using the newly developed and validated test, ‘Ca. P. pruni’ was not found in any of the 434 field samples collected from different plants species grown in different regions of Slovenia. Keywords: phytoplasma, X-disease, real-time PCR, Prunus Published in DiRROS: 22.07.2024; Views: 176; Downloads: 165
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