1. Making PBPK models more reproducible in practiceElena Domínguez-Romero, Stanislav Mazurenko, Martin Scheringer, Vitor A. P. Martins dos Santos, Chris T Evelo, Mihail Anton, John M. Hancock, Anže Županič, Maria Suarez-Diez, 2024, izvirni znanstveni članek Povzetek: Systems biology aims to understand living organisms through mathematically modeling their behaviors at different organizational levels, ranging from molecules to populations. Modeling involves several steps, from determining the model purpose to developing the mathematical model, implementing it computationally, simulating the model’s behavior, evaluating, and refining the model. Importantly, model simulation results must be reproducible, ensuring that other researchers can obtain the same results after writing the code de novo and/or using different software tools. Guidelines to increase model reproducibility have been published. However, reproducibility remains a major challenge in this field. In this paper, we tackle this challenge for physiologically-based pharmacokinetic (PBPK) models, which represent the pharmacokinetics of chemicals following exposure in humans or animals. We summarize recommendations for PBPK model reporting that should apply during model development and implementation, in order to ensure model reproducibility and comprehensibility. We make a proposal aiming to harmonize abbreviations used in PBPK models. To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of MATLAB code converted to Systems Biology Markup Language format using MOCCASIN. As directions for future improvement, more tools to convert computational PBPK models from different software platforms into standard formats would increase the interoperability of these models. The application of other systems biology standards to PBPK models is encouraged. This work is the result of an interdisciplinary collaboration involving the ELIXIR systems biology community. More interdisciplinary collaborations like this would facilitate further harmonization and application of good modeling practices in different systems biology fields. Ključne besede: pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology Objavljeno v DiRROS: 07.11.2024; Ogledov: 26; Prenosov: 12 Celotno besedilo (1,06 MB) Gradivo ima več datotek! Več... |
2. On the presence of the less known arminid nudibranch Dermatobranchus rubidus (Gould, 1852) in the Adriatic SeaTea Knapič, Rino Stanić, Borut Mavrič, Lovrenc Lipej, 2024, izvirni znanstveni članek Povzetek: Two cases of the occurrence of the alien heterobranch species, Dermatobranchus rubidus (Gould, 1852) are reported for the Adriatic Sea. The first record originates from June 2019 from the island of Brač (Croatia, Middle Adriatic Sea), when a specimen was found during the collection of clams, while the second specimen was sighted at Fiesa (Gulf of Trieste, Northern Adriatic Sea) in October 2023, photographed on coarse sand bottom. These are the first records for the Adriatic Sea and indications of the possible establishment of this species in the Mediterranean Sea. Due to its cryptic behaviour and perhaps nocturnal habits, it is difficult to assess whether the species has been overlooked so far or whether it is extending its distribution in the Mediterranean. Ključne besede: first Adriatic record, occurrence Objavljeno v DiRROS: 06.11.2024; Ogledov: 40; Prenosov: 15 Celotno besedilo (1,19 MB) Gradivo ima več datotek! Več... |
3. Impact of indoor air pollution on DNA damage and chromosome stability : a systematic reviewLuka Kazensky, Katarina Matković, Marko Gerić, Bojana Žegura, Gordana Pehnec, Goran Gajski, 2024, pregledni znanstveni članek Povzetek: Indoor air pollution is becoming a rising public health problem and is largely resulting from the burning of solid fuels and heating in households. Burning these fuels produces harmful compounds, such as particulate matter regarded as a major health risk, particularly affecting the onset and exacerbation of respiratory diseases. As exposure to polluted indoor air can cause DNA damage including DNA sd breaks as well as chromosomal damage, in this paper, we aim to provide an overview of the impact of indoor air pollution on DNA damage and genome stability by reviewing the scientific papers that have used the comet, micronucleus, and γ-H2AX assays. These methods are valuable tools in human biomonitoring and for studying the mechanisms of action of various pollutants, and are readily used for the assessment of primary DNA damage and genome instability induced by air pollutants by measuring different aspects of DNA and chromosomal damage. Based on our search, in selected studies (in vitro, animal models, and human biomonitoring), we found generally higher levels of DNA strand breaks and chromosomal damage due to indoor air pollutants compared to matched control or unexposed groups. In summary, our systematic review reveals the importance of the comet, micronucleus, and γ-H2AX assays as sensitive tools for the evaluation of DNA and genome damaging potential of different indoor air pollutants. Additionally, research in this particular direction is warranted since little is still known about the level of indoor air pollution in households or public buildings and its impact on genetic material. Future studies should focus on research investigating the possible impact of indoor air pollutants in complex mixtures on the genome and relate pollutants to possible health outcomes. Ključne besede: indoor air quality, genome damage, comet assay, micronucleus assay, γ-H2AX assay, health risk Objavljeno v DiRROS: 06.11.2024; Ogledov: 43; Prenosov: 15 Celotno besedilo (825,18 KB) Gradivo ima več datotek! Več... |
4. Evidence driven indoor air quality improvement : an innovative and interdisciplinary approach to improving indoor air qualityMario Lovrić, Goran Gajski, Jessica Fernández-Agüera, Mira Pöhlker, Bojana Žegura, Matjaž Novak, Alja Štern, Katja Kološa, Martina Štampar, 2024, pregledni znanstveni članek Povzetek: Indoor air pollution is a recognized emerging threat, claiming millions of lives annually. People are constantly exposed to ambient and indoor air pollution. The latest research shows that people in developed countries spend up to 90% of their time indoors and almost 70% at home. Although impaired IAQ represents a significant health risk, it affects people differently, and specific populations are more vulnerable: children, the elderly, and people with respiratory illnesses are more sensitive to these environmental risks. Despite rather extensive research on IAQ, most of the current understanding about the subject, which includes pollution sources, indoor–outdoor relationships, and ventilation/filtration, is still quite limited, mainly because air quality monitoring in the EU is primarily focused on ambient air quality and regulatory requirements are lacking for indoor environments. Therefore, the EDIAQI project aims to improve guidelines and awareness for advancing the IAQ in Europe and beyond by allowing user-friendly access to information about indoor air pollution exposures, sources, and related risk factors. The solution proposed with EDIAQI consists of conducting a characterization of sources and routes of exposure and dispersion of chemical, biological, and emerging indoor air pollution in multiple cities in the EU. The project will deploy cost-effective/user-friendly monitoring solutions to create new knowledge on sources, exposure routes, and indoor multipollutant body burdens. The EDIAQI project brings together 18 organizations from 11 different European countries that provide interdisciplinary skills and expertise in various fields, including environmental science and technology, medicine, and toxicology, as well as policy design and public engagement. Ključne besede: indoor air pollution, health risk, vulnerable populations, IAQ (Indoor Air Quality), EDIAQI project, monitoring solutions, exposure routes Objavljeno v DiRROS: 06.11.2024; Ogledov: 40; Prenosov: 19 Celotno besedilo (2,15 MB) Gradivo ima več datotek! Več... |
5. Editorial : Mechanisms of plant host resistance against virusesRégis L. Corrêa, Marko Petek, Maite F. S. Vaslin, 2024, drugi znanstveni članki Ključne besede: plants, pathogens, plant viruses, resistance, biotechnological tools, CRISPR/Cas9, agriculture, biotechnology Objavljeno v DiRROS: 05.11.2024; Ogledov: 31; Prenosov: 15 Celotno besedilo (282,18 KB) Gradivo ima več datotek! Več... |
6. Environmental DNA metabarcoding of cephalopod diversity in the Tyrrhenian deep seaMartina La Torre, Alex Cussigh, Valentina Crobe, Martina Spiga, Alice Ferrari, Alessia Cariani, Federica Piattoni, Federica Costantini, Silvia Franzellitti, Alberto Pallavicini, David Stanković, Sergio Stefanni, 2024, izvirni znanstveni članek Povzetek: The deep sea, the largest biome on Earth, is the least explored and understood. This lack of knowledge hampers our ability to understand and protect this important environment. In this study, water and sediment samples were collected at different depths in the central Mediterranean (224–780 m), specifically, within the Dohrn Canyon and the Palinuro Seamount, to investigate the diversity of cephalopods and establish a baseline knowledge of their distribution in these sites to preserve their habitats and estimate the impacts of human-driven environmental changes. Key taxa identified included Heteroteuthis sp., Loligo sp., and Histioteuthis sp., which were the most abundant across all sampling stations. A low overlap in species detection was observed between water and sediment samples, confirming previous findings that the typology of environmental matrices used in eDNA metabarcoding has a significant impact on the organisms detected and, therefore, the integrated use of different matrices to better represent local biodiversity is recommended. Furthermore, this study highlights the limitations posed by gaps in reference databases, particularly for deep-sea organisms, and addresses these by emphasising the need for improved multi-marker approaches and expanded reference databases to enhance the accuracy of eDNA-based biodiversity assessment. Ključne besede: eDNA metabarcoding, cephalopod assemblages, deep-sea biodiversity, Dohrn canyo, environmental matrices, reference databases, Tyrrhenian deep sea, Mediterranean deep sea Objavljeno v DiRROS: 24.10.2024; Ogledov: 54; Prenosov: 33 Celotno besedilo (1,79 MB) Gradivo ima več datotek! Več... |
7. Sustainability assessment of brown trout populations in Serbia (Central Balkans) using the modified ESHIPPO modelTijana Veličković, Saša Marić, David Stanković, Aleksandra Milošković, Milena Radenković, Radek Šanda, Jasna Vukić, Simona Đuretanović, 2024, izvirni znanstveni članek Povzetek: In the inland waters of the Balkans, many brown trout populations have been severely depleted. Therefore, identifying potential threats to their continued survival and ranking populations based on their biological and evolutionary importance enables setting conservation priorities. To assess the sustainability of the brown trout populations in the territory of Serbia (central Balkans), a modification of the ESHIPPO model was performed. The main modification involves incorporating the investigated populations’ genetic structure into the model. Therefore, the new ESHIPPOsalmo model includes an analysis of biological parameters and the impact of multiple factors, including habitat alterations, invasive species, pollution, human population growth, and over-exploitation. In order to investigate individual levels of influence of the model’s analyzed parameters, a combination of supervised and unsupervised machine learning methods was used. The structure of the model is based on general and easily measurable indicators, which enables its application in any salmonid river in the world. By evaluating the parameters of the ESHIPPOsalmo model, we were able to establish that, of the analyzed populations from 46 localities, 37% have a moderate level of sustainability, 43% low, and 20% critically low. Ključne besede: brown trout, conservation, genetic structure, habitat alterations, invasive species, sustainability Objavljeno v DiRROS: 23.10.2024; Ogledov: 91; Prenosov: 46 Celotno besedilo (4,15 MB) Gradivo ima več datotek! Več... |
8. 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, izvirni znanstveni članek Povzetek: 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. Ključne besede: algal blooms, diatoms, virus, PnGalRNAV, genome, Adriatic Sea, marine virology, phytoplankton ecology, marine biology Objavljeno v DiRROS: 23.10.2024; Ogledov: 52; Prenosov: 25 Celotno besedilo (8,37 MB) Gradivo ima več datotek! Več... |
9. 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, izvirni znanstveni članek Povzetek: 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. Ključne besede: microplastics, sediments, Gulf of Trieste, density separation, polypropylene, accumulation of pollutants, marine biology Objavljeno v DiRROS: 23.10.2024; Ogledov: 50; Prenosov: 26 Celotno besedilo (1,77 MB) Gradivo ima več datotek! Več... |
10. Animal life in the shallow subseafloor crust at deep-sea hydrothermal ventsMonika Bright, Sabine Gollner, André Luiz de Oliveira, Salvador Espada-Hinojosa, Avery Fulford, Tihomir Makovec, Tinkara Tinta, 2024, izvirni znanstveni članek Povzetek: It was once believed that only microbes and viruses inhabited the subseafloor crust beneath hydrothermal vents. Yet, on the seafloor, animals like the giant tubeworm Riftia pachyptila thrive. Their larvae are thought to disperse in the water column, despite never being observed there. We hypothesized that these larvae travel through the subseafloor via vent fluids. In our exploration, lifting lobate lava shelves revealed adult tubeworms and other vent animals in subseafloor cavities. The discovery of vent endemic animals below the visible seafloor shows that the seafloor and subseafloor faunal communities are connected. The presence of adult tubeworms suggests larval dispersal through the recharge zone of the hydrothermal circulation system. Given that many of these animals are host to dense bacterial communities that oxidize reduced chemicals and fix carbon, the extension of animal habitats into the subseafloor has implications for local and regional geochemical flux measurements. These findings underscore the need for protecting vents, as the extent of these habitats has yet to be fully ascertained. Ključne besede: subseafloor, hydrothermal vents, tubeworms, larvae, vent fluids, bacterial communities, geochemical flux, geochemistry, marine biology Objavljeno v DiRROS: 22.10.2024; Ogledov: 80; Prenosov: 33 Celotno besedilo (4,15 MB) Gradivo ima več datotek! Več... |