621. A new network for the advancement of marine biotechnology in Europe and beyondAna Rotter, Ariola Bacu, Michèle Barbier, Francesco Bertoni, Atle M. Bones, M. Leonor Cancela, Jens Carlsson, Maria F. Carvalho, Marta Cegłowska, Meltem Conk Dalay, Jerica Sabotič, 2020, izvirni znanstveni članek Povzetek: Marine organisms produce a vast diversity of metabolites with biological activities useful for humans, e.g., cytotoxic, antioxidant, anti-microbial, insecticidal, herbicidal, anticancer, pro-osteogenic and pro-regenerative, analgesic, anti-inflammatory, anti-coagulant, cholesterol-lowering, nutritional, photoprotective, horticultural or other beneficial properties. These metabolites could help satisfy the increasing demand for alternative sources of nutraceuticals, pharmaceuticals, cosmeceuticals, food, feed, and novel bio-based products. In addition, marine biomass itself can serve as the source material for the production of various bulk commodities (e.g., biofuels, bioplastics, biomaterials). The sustainable exploitation of marine bio-resources and the development of biomolecules and polymers are also known as the growing field of marine biotechnology. Up to now, over 35,000 natural products have been characterized from marine organisms, but many more are yet to be uncovered, as the vast diversity of biota in the marine systems remains largely unexplored. Since marine biotechnology is still in its infancy, there is a need to create effective, operational, inclusive, sustainable, transnational and transdisciplinary networks with a serious and ambitious commitment for knowledge transfer, training provision, dissemination of best practices and identification of the emerging technological trends through science communication activities. A collaborative (net)work is today compelling to provide innovative solutions and products that can be commercialized to contribute to the circular bioeconomy. This perspective article highlights the importance of establishing such collaborative frameworks using the example of Ocean4Biotech, an Action within the European Cooperation in Science and Technology (COST) that connects all and any stakeholders with an interest in marine biotechnology in Europe and beyond. Ključne besede: marine biotechnology, marine natural products, blue growth, marine biodiversity and chemodiversity, responsible research and innovation, stakeholder engagement, science communication, sustainability Objavljeno v DiRROS: 22.07.2024; Ogledov: 129; Prenosov: 72
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622. Digital PCR method for detection and quantification of specific antimicrobial drug-resistance mutations in human cytomegalovirusAlexandra Bogožalec Košir, Tašja Cvelbar, Martin Kammel, Hans-Peter Grunert, Heinz Zeichhardt, Mojca Milavec, 2020, izvirni znanstveni članek Povzetek: Antimicrobial drug resistance is one of the biggest threats to human health worldwide. Timely detection and quantification of infectious agents and their susceptibility to antimicrobial drugs are crucial for efficient management of resistance to antiviral drugs. In clinical settings, viral drug resistance is most often associated with prolonged treatment of chronic infections, and assessed by genotyping methods; e.g., sequencing and PCR. These approaches have limitations: sequencing can be expensive and does not provide quantification; and qPCR quantification is hampered by a lack of reference materials for standard curves. In recent years, digital PCR has been introduced, which provides absolute quantification without the need for reference materials for standard curves. Using digital PCR, we have developed a rapid, sensitive and accurate method for genotyping and quantification of the most prevalent mutations that cause human cytomegalovirus resistance to ganciclovir. Ključne besede: digital PCR, antimicrobial-drug resistance, HCMV, polymerase chain reaction, viruses Objavljeno v DiRROS: 22.07.2024; Ogledov: 126; Prenosov: 105
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623. European policies and legislation targeting ocean acidification in european waters : current stateCharles Galdies, Richard Bellerby, Donata Melaku Canu, Wenting Chen, Alenka Malej, 2020, izvirni znanstveni članek Povzetek: Ocean acidification (OA) is a global problem with profoundly negative environmental, social and economic consequences. From a governance perspective, there is a need to ensure a coordinated effort to directly address it. This study reviews 90 legislative documents from 17 countries from the European Economic Area (EEA) and the UK that primarily border the sea. The primary finding from this study is that the European national policies and legislation addressing OA is at best uncoordinated. Although OA is acknowledged at the higher levels of governance, its status as an environmental challenge is greatly diluted at the European Union Member State level. As a notable exception within the EEA, Norway seems to have a proactive approach towards legislative frameworks and research aimed towards further understanding OA. On the other hand, there was a complete lack of, or inadequate reporting in the Marine Strategy Framework Directive by the majority of the EU Member States, with the exception of Italy and the Netherlands. We argue that the problems associated with OA and the solutions needed to address it are unique and cannot be bundled together with traditional climate change responses and measures. Therefore, European OA-related policy and legislation must reflect this and tailor their actions to mitigate OA to safeguard marine ecosystems and societies. A stronger and more coordinated approach is needed to build environmental, economic and social resilience of the observed and anticipated changes to the coastal marine systems. Objavljeno v DiRROS: 22.07.2024; Ogledov: 96; Prenosov: 65
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624. Functional imaging of the ocular fundus using an 8-band retinal multispectral imaging systemJ. Emanuel Ramos de Carvalho, Richelle J. M. Hoveling, Cornelis J. F. van Noorden, Reinier O. Schlingemann, Maurice C. G. Aalders, 2020, izvirni znanstveni članek Povzetek: Application of functional imaging in ophthalmology requires efficient imaging techniques that can detect and quantify chromophores to visualise processes in vivo. The aim of the present study was to develop and evaluate a fast and affordable imaging system. We describe an eight-band retinal multispectral imaging (MSI) system and compare it with a hyperspectral imaging (HSI) device. Determination of blood oxygen saturation was studied as proof of principle. Reflectance of incident light is measured as 1/absorbance at different wavelengths between 440 nm and 580 nm. Both devices have incorporated optical bandpass filters in a mydriatic fundus camera. The MSI system scans the retina at eight pre-defined wavelengths specific for the spectrum of haemoglobin. The HSI system acquires a full scan from 480 to 720 nm in 5 nm steps. A simple assessment of the ratio between the absorbance peaks of oxygenated haemoglobin (HbO2) and reduced haemoglobin (HbR) was not suitable for generating validated oxygenation maps of the retina. However, a correction algorithm that compares the measured reflectance with reflectance spectra of fully oxygenated and fully deoxygenated blood allowed our MSI setup to estimate relative oxygen saturation at higher levels, but underestimated relative oxygen saturation at lower levels. The MSI device generated better quality images than the HSI device. It allows customisation with filter sets optimised for other chromophores of interest, and augmented with extrinsic contrast imaging agents, it has the potential for a wider range of ophthalmic molecular imaging applications. Ključne besede: functional imaging, multispectral imaging, hyperspectral imaging, oximetry Objavljeno v DiRROS: 22.07.2024; Ogledov: 406; Prenosov: 263
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625. Biogeographical history of golden orbweavers : chronology of a global conquestEva Turk, Klemen Čandek, Simona Kralj-Fišer, Matjaž Kuntner, 2020, izvirni znanstveni članek Povzetek: Aim
A wholistic biogeographical reconstruction should combine a phylogeny with specifics of organismal biology, plate tectonics and consequent probabilities of historic dispersal events. Here, we demonstrate this approach by reconstructing the geographical origin and sequence of intercontinental colonization of the golden orbweaving spiders, a global clade. We test two alternative hypotheses about their ancestral range. Due to the highest contemporary species diversity in Africa, the ‘Out of Africa’ hypothesis predicts the Afrotropics as their most likely ancestral area. The alternative, ‘Out of West Burma’ hypothesis aims to explain a Burmese amber fossil as stem nephilid. Because the West Burma block probably detached from Australia, then rafted towards Laurasia, either on its own or with India, this hypothesis predicts either Australasia or Indomalaya (or both) as the ancestral area.
Location
Worldwide.
Taxon
Golden orbweaving spiders, family Nephilidae.
Methods
We construct an expanded phylogeny of nephilid spiders and apply RASP (Reconstruct Ancestral State in Phylogenies) to infer their global biogeographical history. We fit the data to six integrated biogeographical models: DEC, DIVALIKE, BAYAREALIKE and their +j variants. We fine-tune the analysis by evaluating varying probabilities of dispersal between geographical areas throughout the clade's evolutionary history. We use the physical distance between the areas as a proxy for dispersal probabilities, thus accounting for plate tectonics.
Results
The best supported model reconstructs both Australasia and Indomalaya as ancestral area. In several parts of the phylogeny, these areas persist for the estimated 130-million-year evolutionary history. However, numerous intercontinental shifts in nephilid biogeographical history are also inferred. Since nephilid origins are clearly Gondwanan, our study supports the interpretations that Burmese amber contains Gondwanan biota.
Main conclusions
These results are consistent with the Out of West Burma hypothesis but reject the Out of Africa hypothesis. That certain clades persist in their ancestral ranges while others may shift continents aligns well with the known nephilid biology. Our methodological approach that assesses organismal specific dispersal probabilities through concrete distances measured though time slices of the Earth's history can be applied to biogeographical reconstruction of any lineage. Ključne besede: spiders, golden orbweavers, Nephilidae, reconstruction of lineage, biogeography Objavljeno v DiRROS: 22.07.2024; Ogledov: 118; Prenosov: 153
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626. Unpublished Mediterranean records of marine alien and cryptogenic speciesStelios Katsanevakis, Dimitris Poursanidis, Domen Trkov, Lovrenc Lipej, Ana Fortič, Martina Orlando-Bonaca, Borut Mavrič, 2020, izvirni znanstveni članek Povzetek: Good datasets of geo-referenced records of alien species are a prerequisite for assessing the spatio-temporal dynamics of biological invasions, their invasive potential, and the magnitude of their impacts. However, with the exception of first records on a country level or wider regions, observations of species presence tend to remain unpublished, buried in scattered repositories or in the personal databases of experts. Through an initiative to collect, harmonize and make such unpublished data for marine alien and cryptogenic species in the Mediterranean Sea available, a large dataset comprising 5376 records was created. It includes records of 239 alien or cryptogenic taxa (192 Animalia, 24 Plantae, 23 Chromista) from 19 countries surrounding the Mediterranean Sea. In terms of records, the most reported Phyla in descending order were Chordata, Mollusca, Chlorophyta, Arthropoda, and Rhodophyta. The most recorded species was Caulerpa cylindracea, followed by Siganus luridus, Magallana sp. (cf. gigas or angulata) and Pterois miles. The dataset includes records from 1972 to 2020, with the highest number of records observed in 2018. Among the records of the dataset, Dictyota acutiloba is a first record for the Mediterranean Sea. Nine first country records are also included: the alga Caulerpa taxifolia var. distichophylla, the cube boxfish Ostracion cubicus, and the cleaner shrimp Urocaridella pulchella from Israel; the sponge Paraleucilla magna from Libya and Slovenia; the lumpfish Cyclopterus lumpus from Cyprus; the bryozoan Celleporaria vermiformis and the polychaetes Prionospio depauperata and Notomastus aberans from Malta. Ključne besede: non-native species, non-indigenous, distribution, citizen science, invasive alien species, geo-referenced records, Mediterranean Sea Objavljeno v DiRROS: 22.07.2024; Ogledov: 111; Prenosov: 111
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627. DINCAE 1.0 : a convolutional neural network with error estimates to reconstruct sea surface temperature satellite observationsAlexander Barth, Aida Alvera-Azcárate, Matjaž Ličer, Jean-Marie Beckers, 2020, izvirni znanstveni članek Povzetek: A method to reconstruct missing data in sea surface temperature data using a neural network is presented. Satellite observations working in the optical and infrared bands are affected by clouds, which obscure part of the ocean underneath. In this paper, a neural network with the structure of a convolutional auto-encoder is developed to reconstruct the missing data based on the available cloud-free pixels in satellite images. Contrary to standard image reconstruction with neural networks, this application requires a method to handle missing data (or data with variable accuracy) in the training phase. The present work shows a consistent approach which uses the satellite data and its expected error variance as input and provides the reconstructed field along with its expected error variance as output. The neural network is trained by maximizing the likelihood of the observed value. The approach, called DINCAE (Data INterpolating Convolutional Auto-Encoder), is applied to a 25-year time series of Advanced Very High Resolution Radiometer (AVHRR) sea surface temperature data and compared to DINEOF (Data INterpolating Empirical Orthogonal Functions), a commonly used method to reconstruct missing data based on an EOF (empirical orthogonal function) decomposition. The reconstruction error of both approaches is computed using cross-validation and in situ observations from the World Ocean Database. DINCAE results have lower error while showing higher variability than the DINEOF reconstruction. Objavljeno v DiRROS: 19.07.2024; Ogledov: 132; Prenosov: 91
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628. One-step reverse-transcription digital PCR for reliable quantification of different pepino mosaic virus genotypesNataša Mehle, Larisa Gregur, Alexandra Bogožalec Košir, David Dobnik, 2020, izvirni znanstveni članek Povzetek: In recent years, pepino mosaic virus (PepMV) has rapidly evolved from an emerging virus to an endemic pathogen, as it causes significant loses to tomato crops worldwide. At present, the main control strategy for prevention of PepMV disease in tomato production remains based on strict hygiene measures. To prevent damage caused by PepMV, cross-protection is used in some countries. Reliable characterisation, detection and quantification of the pathogen are vital for disease control. At present, reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) is generally used for this purpose. However, quantitative use of RT-qPCR is linked to standardised reference materials, which are not available for PepMV. In addition, many factors can influence RT-qPCR efficiencies and lead to lower accuracy of the quantification. In this study, well-characterised PepMV-genotype-specific RT-qPCR assays were transferred to two digital PCR (dPCR) platforms. dPCR-based assays allow absolute quantification without the need for standard curves, and due to the binary nature of the reaction, dPCR also overcomes many of the other drawbacks of RT-qPCR. We have shown that these newly developed and validated PepMV-genotype-specific dPCR assays are suitable candidates for higher-order methods for quantification of PepMV RNA, as they show lower measurement variability, with sensitivity and specificity comparable to RT-qPCR. Ključne besede: digital PCR, pepino mosaic virus, quantification, genotype specific Objavljeno v DiRROS: 19.07.2024; Ogledov: 140; Prenosov: 56
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629. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environmentKatarina Bačnik, Denis Kutnjak, Anja Pecman, Nataša Mehle, Magda Tušek-Žnidarič, Ion Gutiérrez-Aguirre, Maja Ravnikar, 2020, izvirni znanstveni članek Povzetek: Viruses represent one of the most important threats to agriculture. Several viral families include highly stable pathogens, which remain infective and can be transported long distances in water. The diversity of plant viruses in wastewater remains understudied; however, their potential impact is increasing with the increased irrigation usage of reclaimed wastewater. To determine the abundance, diversity and biological relevance of plant viruses in wastewater influents and effluents we applied an optimized virus concentration method followed by high-throughput sequencing and infectivity assays. We detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), which remain infective even after conventional wastewater treatment. These results demonstrate the potential of metagenomics to capture the diversity of plant viruses circulating in the environment and expose the potential risk of the uncontrolled use of reclaimed water for irrigation. Ključne besede: wastewater, virome, high-throughput sequencing, plant viruses, tobamoviruses, infectivity Objavljeno v DiRROS: 19.07.2024; Ogledov: 249; Prenosov: 148
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630. Cancer-related fatigue : causes and current treatment optionsMelissa S. Y. Thong, Cornelis J. F. van Noorden, Karen Steindorf, Volker Arndt, 2020, izvirni znanstveni članek Povzetek: Fatigue is a symptom commonly experienced by survivors of cancer through all stages of the disease trajectory. Survivors identify fatigue as a significant problem which is not adequately addressed by healthcare providers [1•]. Being fatigued has a greater negative impact on functioning and health-related quality of life (HRQoL) than other symptoms such as pain or depression [2, 3]. Fatigued survivors are more likely to have reduced employment participation [4, 5], greater financial stress [6], and higher healthcare utilization [6, 7]. Moreover, fatigue may reduce survival; feeling fatigued at diagnosis [6, 8] and during survivorship [9] is associated with higher mortality.
This review aims to provide a summary on the current state of research on cancer-related fatigue (CRF) of survivors with local disease treated with curative intent. We briefly summarize the prevalence, definition, evaluation, and etiology of CRF. Due to the volume of research on CRF treatments, we provide a non-exhaustive overview of treatments for CRF published within the last 5 years (guidelines, meta-analyses, reviews, randomized trials). Ključne besede: cancer-related fatigue, cytokines, physical activity, pharmacologic, complementary and alternative medicine Objavljeno v DiRROS: 19.07.2024; Ogledov: 127; Prenosov: 91
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