21. Inter-comparison of marine microbiome sampling protocolsFrancisco Pascoal, Maria Paola Tomasino, Roberta Piredda, Grazia Marina Quero, Luís Torgo, Julie Poulain, Tinkara Tinta, Timotej Turk Dermastia, 2023, izvirni znanstveni članek Povzetek: Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22–3 µm, 3–20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.
Ključne besede: marine microbiome, standardized sampling, inter-comparison, amplicon sequencing, microbial diversity, seawater sampling
Objavljeno v DiRROS: 12.07.2024; Ogledov: 11; Prenosov: 5
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22. Identification of marine biotechnology value chains with high potential in the Northern Mediterranean regionAna Rotter, Antonia Giannakourou, Jesús E. Argente García, Grazia Marina Quero, Charlène Auregan, Ernesta Grigalionyte-Bembič, Jan Ulčar, 2023, izvirni znanstveni članek Povzetek: Marine (blue) biotechnology is an emerging field enabling the valorization of new products and processes with massive potential for innovation and economic growth. In the Mediterranean region, this innovation potential is not exploited as well as in other European regions due to a lack of a clear identification of the different value chains and the high fragmentation of business innovation initiatives. As a result, several opportunities to create an innovative society are being missed. To address this problem, eight Northern Mediterranean countries (Croatia, France, Greece, Italy, Montenegro, Portugal, Slovenia and Spain) established five national blue biotechnology hubs to identify and address the bottlenecks that prevent the development of marine biotechnology in the region. Following a three-step approach (1. Analysis: setting the scene; 2. Transfer: identification of promising value chains; 3. Capitalization: community creation), we identified the three value chains that are most promising for the Northern Mediterranean region: algae production for added-value compounds, integrated multi-trophic aquaculture (IMTA) and valorization aquaculture/fisheries/processing by-products, unavoidable/unwanted catches and discards. The potential for the development and the technical and non-technical skills that are necessary to advance in this exciting field were identified through several stakeholder events which provided valuable insight and feedback that should be addressed for marine biotechnology in the Northern Mediterranean region to reach its full potential.
Ključne besede: marine biotechnology, blue biotechnology, innovation, value chains, Northern Mediterranean, microalgae, macroalgae, IMTA, circular economy, discards valorization
Objavljeno v DiRROS: 12.07.2024; Ogledov: 10; Prenosov: 6
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23. Aberrantly expressed hsa_circ_0060762 and CSE1L as potential peripheral blood biomarkers for ALSMetka Ravnik-Glavač, Massimo Mezzavilla, Ana Dolinar, Blaž Koritnik, Damjan Glavač, 2023, izvirni znanstveni članek Povzetek: Amyotrophic lateral sclerosis (ALS) is a rapidly progressive adult-onset neurodegenerative disease that is often diagnosed with a delay due to initial non-specific symptoms. Therefore, reliable and easy-to-obtain biomarkers are an absolute necessity for earlier and more accurate diagnostics. Circular RNAs (circRNAs) have already been proposed as potential biomarkers for several neurodegenerative diseases. In this study, we further investigated the usefulness of circRNAs as potential biomarkers for ALS. We first performed a microarray analysis of circRNAs on peripheral blood mononuclear cells of a subset of ALS patients and controls. Among the differently expressed circRNA by microarray analysis, we selected only the ones with a host gene that harbors the highest level of conservation and genetic constraints. This selection was based on the hypothesis that genes under selective pressure and genetic constraints could have a major role in determining a trait or disease. Then we performed a linear regression between ALS cases and controls using each circRNA as a predictor variable. With a False Discovery Rate (FDR) threshold of 0.1, only six circRNAs passed the filtering and only one of them remained statistically significant after Bonferroni correction: hsa_circ_0060762 and its host gene CSE1L. Finally, we observed a significant difference in expression levels between larger sets of patients and healthy controls for both hsa_circ_0060762 and CSE1L. CSE1L is a member of the importin β family and mediates inhibition of TDP-43 aggregation; the central pathogenicity in ALS and hsa_circ_0060762 has binding sites for several miRNAs that have been already proposed as biomarkers for ALS. In addition, receiver operating characteristics curve analysis showed diagnostic potential for CSE1L and hsa_circ_0060762. Hsa_circ_0060762 and CSE1L thus represent novel potential peripheral blood biomarkers and therapeutic targets for ALS.
Ključne besede: amyotrophic lateral sclerosis, ALS, circRNA, biomarker, peripheral blood biomarker, hsa_circ_0060762, CSE1L, biomedicine
Objavljeno v DiRROS: 12.07.2024; Ogledov: 11; Prenosov: 7
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24. An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populationsJody Robbemont, Sam van Veldhuijzen, Steven J. R. Allain, Johanna Ambu, Ryan Boyle, David Stanković, 2023, izvirni znanstveni članek Povzetek: Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding.
Ključne besede: citizen science, Ichthyosaura alpestris, invasive species, mtDNA barcoding, skin swabbing
Objavljeno v DiRROS: 12.07.2024; Ogledov: 7; Prenosov: 4
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25. Dissolved gaseous mercury production and sea-air gaseous exchange in impacted coastal environments of the northern Adriatic SeaFederico Floreani, Nicolò Barago, Katja Klun, Jadran Faganeli, Stefano Covelli, 2023, izvirni znanstveni članek Povzetek: The northern Adriatic Sea is well known for mercury (Hg) contamination mainly due to historical Hg mining which took place in Idrija (Slovenia). The formation of dissolved gaseous mercury (DGM) and its subsequent volatilisation can reduce the amount of Hg available in the water column. In this work, the diurnal patterns of both DGM production and gaseous elemental Hg (Hg0) fluxes at the water-air interface were seasonally evaluated in two selected environments within this area, a highly Hg-impacted, confined fish farm (VN: Val Noghera, Italy) and an open coastal zone less impacted by Hg inputs (PR: Bay of Piran, Slovenia). A floating flux chamber coupled with a real-time Hg0 analyser was used for flux estimation in parallel with DGM concentrations determination through in-field incubations. Substantial DGM production was observed at VN (range = 126.0–711.3 pg L−1) driven by both strong photoreduction and possibly dark biotic reduction, resulting in higher values in spring and summer and comparable concentrations throughout both day and night. Significantly lower DGM was observed at PR (range = 21.8–183.4 pg L−1). Surprisingly, comparable Hg0 fluxes were found at the two sites (range VN = 7.43–41.17 ng m−2 h−1, PR = 0–81.49 ng m−2 h−1), likely due to enhanced gaseous exchanges at PR thanks to high water turbulence and to the strong limitation of evasion at VN by water stagnation and expected high DGM oxidation in saltwater. Slight differences between the temporal variation of DGM and fluxes indicate that Hg evasion is more controlled by factors such as water temperature and mixing conditions than DGM concentrations alone. The relative low Hg losses through volatilisation at VN (2.4–4.6% of total Hg) further confirm that static conditions in saltwater environments negatively affect the ability of this process in reducing the amount of Hg retained in the water column, therefore potentially leading to a greater availability for methylation and trophic transfer.
Ključne besede: Idrija mercury mine, mercury evasion, fish farm, flux chamber, water-air exchange, Adriatic Sea, Idrijski rudnik živega srebra, ribogojnica, pretočna komora, izmenjava voda-zrak, Jadransko morje
Objavljeno v DiRROS: 12.07.2024; Ogledov: 6; Prenosov: 3
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26. Cytotoxicity and antibacterial efficacy of betaine- and choline-substituted polymersLucija Jurko, Damjan Makuc, Alja Štern, Janez Plavec, Bojana Žegura, Perica Bošković, Rupert Kargl, 2023, izvirni znanstveni članek Povzetek: Cationic charge has been widely used to increase polymer adsorption and flocculation of dispersions or to provide antimicrobial activity. In this work, cationization of hydroxyethyl cellulose (HEC) and polyvinyl alcohol (PVA) was achieved by covalently coupling betaine hydrochloride and choline chloride to the polymer backbones through carbonyl diimidazole (CDI) activation. Two approaches for activation were investigated. CDI in excess was used to activate the polymers’ hydroxyls followed by carbonate formation with choline chloride, or CDI was used to activate betaine hydrochloride, followed by ester formation with the polymers’ hydroxyls. The first approach led to a more significant cross-linking of PVA, but not of HEC, and the second approach successfully formed ester bonds. Cationic, nitrogen-bearing materials with varying degrees of substitution were obtained in moderate to high yields. These materials were analyzed by Fourier transform infrared spectroscopy, nuclear magnetic resonance, polyelectrolyte titration, and kaolin flocculation. Their dose-dependent effect on the growth of Staphylococcus aureus and Pseudomonas aeruginosa, and L929 mouse fibroblasts, was investigated. Significant differences were found between the choline- and betaine-containing polymers, and especially, the choline carbonate esters of HEC strongly inhibited the growth of S. aureus in vitro but were also cytotoxic to fibroblasts. Fibroblast cytotoxicity was also observed for betaine esters of PVA but not for those of HEC. The materials could potentially be used as antimicrobial agents for instance by coating surfaces, but more investigations into the interaction between cells and polysaccharides are necessary to clarify why and how bacterial and human cells are inhibited or killed by these derivatives, especially those containing choline.
Ključne besede: hydroxyethyl cellulose, polyvinyl alcohol, antimicrobial, S. aureus, P. aeruginosa, L929 mouse fibroblast, cationic polymer
Objavljeno v DiRROS: 12.07.2024; Ogledov: 18; Prenosov: 5
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27. Managing the deluge of newly discovered plant viruses and viroids : an optimized scientific and regulatory framework for their characterization and risk analysisNuria Fontdevila Pareta, Maryam Khalili, Ayoub Maachi, Mark Paul Selda Rivarez, Johan Rollin, Ferran Salavert Pamblanco, Coline Temple, Miguel A. Aranda, Denis Kutnjak, Maja Ravnikar, 2023, izvirni znanstveni članek Povzetek: The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
Ključne besede: plant viruses and viroids, high throughput sequencing (HTS), biological characterization, plant health, regulatory agencies, Pest Risk Analysis (PRA), virus disease
Objavljeno v DiRROS: 12.07.2024; Ogledov: 10; Prenosov: 3
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28. Consensus molecular subtypes (CMS) in metastatic colorectal cancer : personalized medicine decisionMartina Reberšek, 2020, pregledni znanstveni članek Povzetek: Colorectal cancer (CRC) is one of the most common types of cancer in the world. Metastatic disease is still incurable in most of these patients, but the survival rate has improved by treatment with novel systemic chemotherapy and targeted therapy in combination with surgery. New knowledge of its complex heterogeneity in terms of genetics, epigenetics, transcriptomics and microenvironment, including prognostic and clinical characteristics, led to its classification into various molecular subtypes of metastatic CRC, called consensus molecular subtypes (CMS). The CMS classification thus enables the medical oncologists to adjust the treatment from case to case. They can determine which type of systemic chemotherapy or targeted therapy is best suited to a specific patient, what dosages are needed and in what order. Conclusions. CMS in metastatic CRC are the new tool to include the knowledge of molecular factors, tumour stroma and signalling pathways for personalized, patient-orientated systemic treatment in precision medicine.
Ključne besede: metastatic colorectal cancer, heterogeneity, biomarkers, consensus molecular subtype
Objavljeno v DiRROS: 12.07.2024; Ogledov: 7; Prenosov: 2
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29. Does regular quality control improve the quality of surgery in Slovenian breast cancer screening program?Andraž Perhavec, Sara Milićević, Barbara Perić, Janez Žgajnar, 2020, izvirni znanstveni članek Povzetek: The aim of our study was to evaluate the quality of surgery of Slovenian breast cancer screening program (DORA) using the requested EU standards. Furthermore, we investigated whether regular quality control over the 3-year period improved the quality of surgical management. Patients and methods. Patients who required surgical management within DORA between January 1st, 2016 and December 31st, 2018 were included in the retrospective study. Quality indicators (QIs) were adjusted mainly according to European Society of Breast Cancer Specialists (EUSOMA) and European Breast Cancer Network (EBCN) recommendations. Five QIs for therapeutic and two for diagnostic surgeries were selected. Additionally, variability in achieving the requested QIs among surgeons was analysed. Results. Between 2016 and 2018, 14 surgeons performed 1421 breast procedures in 1398 women. There were 1197 therapeutical (for proven breast cancer) and 224 diagnostic surgical interventions respectively. Overall, the minimal standard was met in two QIs for therapeutic and none for diagnostic procedures. A statistically significant improvement in three QIs for therapeutic and in one QI for diagnostic procedures was observed however, indicating that regular quality control improves the quality of surgery. A high variability in achieving the requested QIs was observed among surgeons, which remained high throughout the study period. Conclusions. Adherence to all selected surgical QIs in patients from screening program is difficult to achieve, especially to those specifically defined for screen-detected lesions. Regular quality control may improve results over time. Reducing the number of surgeons dedicated to breast pathology may reduce variability of management inside the institution.
Ključne besede: breast surgery, mammography, screening program, quality control
Objavljeno v DiRROS: 12.07.2024; Ogledov: 9; Prenosov: 4
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30. Significance of nuclear factor - kappa beta activation on prostate needle biopsy samples in the evaluation of Gleason score 6 prostatic carcinoma indolenceMarko Zupančič, Boris Pospihalj, Snežana Cerović, Barbara Gazić, Primož Drev, Marko Hočevar, Andraž Perhavec, 2020, izvirni znanstveni članek Povzetek: The goal of our study was to find out whether the immunohistochemical expression of nuclear factor-kappa beta (NF-%B) p65 in biopsy samples with Gleason score 3 + 3 = 6 (GS 6) can be a negative predictive factor for Prostate cancer (PCa) indolence. Patients and methods Study was conducted on a retrospective cohort of 123 PCa patients with initial total PSA % 10 ng/ml, number of needle biopsy specimens % 8, GS 6 on biopsy and T1/T2 estimated clinical stage who underwent laparoscopic radical prostatectomy and whose archived formalin-fixed and paraffin-embedded (FFPE) prostate needle biopsy specimens were used for additional immunohistochemistry staining for detection of NF-%B p65. Both cytoplasmic and nuclear NF-%B p65 expression in biopsy cores with PCa were correlated with postoperative pathological stage, positive surgical margins, GS and biochemical progression of disease. Results After follow-up of 66 months, biochemical progression (PSA % 0.2 ng/ml) occurred in 6 (5.1%) patients, 3 (50%) with GS 6 and 3 (50%) with GS 7 after radical prostatectomy. Both cytoplasmic and nuclear NF-%B p65 expressions were not significantly associated with pathological stage, positive surgical margin and postoperative GS. Patients with positive cytoplasmic NF-kB reaction had significantly more frequent biochemical progression than those with negative cytoplasmic NF-kB reaction with PSA 0.2 ng/ml as cutoff point (p = 0.015) and a trend towards more biochemical progression with PSA % 0.05 ng/ml as cutoff point (p = 0.068). Conclusions Cytoplasmic expression of NF-%B is associated with more biochemical progression and might be an independent prognostic factor for recurrence-free survival (RFS), but further studies including larger patient cohorts are needed to confirm these initial results.
Ključne besede: prostate cancer, needle biopsy, nuclear factor-kappa beta, Gleason
Objavljeno v DiRROS: 12.07.2024; Ogledov: 5; Prenosov: 2
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