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Abstract: 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.
Keywords: marine microbiome, standardized sampling, inter-comparison, amplicon sequencing, microbial diversity, seawater sampling
Published in DiRROS: 12.07.2024; Views: 278; Downloads: 258
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Abstract: 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.
Keywords: amyotrophic lateral sclerosis, ALS, circRNA, biomarker, peripheral blood biomarker, hsa_circ_0060762, CSE1L, biomedicine
Published in DiRROS: 12.07.2024; Views: 254; Downloads: 210
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Abstract: 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.
Keywords: 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
Published in DiRROS: 12.07.2024; Views: 293; Downloads: 220
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Abstract: 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.
Keywords: plant viruses and viroids, high throughput sequencing (HTS), biological characterization, plant health, regulatory agencies, Pest Risk Analysis (PRA), virus disease
Published in DiRROS: 12.07.2024; Views: 325; Downloads: 145
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Abstract: 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.
Keywords: breast surgery, mammography, screening program, quality control
Published in DiRROS: 12.07.2024; Views: 245; Downloads: 94
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