31. Harmonizing microstructures and enhancing mechanical resilience : novel powder metallurgy approach for Zn–Mg alloysAnna Boukalová, Jiří Kubásek, David Nečas, Peter Minárik, Črtomir Donik, Drahomír Dvorský, Dalibor Vojtěch, Alena Michalcová, Matjaž Godec, Irena Paulin, 2024, original scientific article Abstract: Zinc alloys are recognised for their excellent biocompatibility and favourable corrosion rates, making them suitable for bioabsorbable implants. However, their mechanical properties necessitate improvement to fulfil the rigorous requirements of biomedical applications. This research focuses on engineering pseudo-harmonic structures within zinc alloys through a comprehensive method combining mechanical alloying, spark plasma sintering, and hot extrusion techniques. This fabrication process results in a composite material characterised by a soft core surrounded by a continuous, three-dimensional, ultrafine-grained hard shell. The experiment involved blending pure zinc with Zn–1Mg alloy powder, leading to the formation of both ductile zinc and fine-grained Zn–1Mg regions. While the Mg2Zn11 intermetallic phase was found to enhance the alloy's mechanical strength, the presence of oxide shells adversely affected the material's properties. The elimination of these shells via hot extrusion markedly improved the alloy's tensile strength, reaching an average value of tensile strength of 333 ± 7 MPa. This study provides significant insights into the material engineering of zinc-based alloys for biodegradable implant applications, demonstrating a viable approach to optimising their mechanical performance. Keywords: zinc, magnesium, biodegradable, powder metallurgy, harmonic structure Published in DiRROS: 23.07.2024; Views: 141; Downloads: 136
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32. Exploring the microstructure, mechanical properties, and corrosion resistance of innovative bioabsorbable Zn-Mg-(Si) alloys fabricated via powder metallurgy techniquesDavid Nečas, Vojtěch Hybášek, Jan Pinc, Andrea Školáková, Ilona Voňavková, Klára Hosová, Martin Zlámal, Anna Boukalová, Jan Pokorný, Drahomír Dvorský, Črtomir Donik, Dalibor Vojtěch, Jiří Kubásek, 2024, original scientific article Abstract: Zinc alloys belong to the widely studied materials for applications like medical devices, however, they often
encounter an inappropriate combination of mechanical/corrosion/biological properties. In this respect, we
produced the Zn–1Mg and Zn–1Mg–1Si containing biologically friendly elements with potential strengthening
effects on zinc matrix by powder metallurgy methods including mechanical alloying, spark plasma sintering, and
extrusion further enabling the formation of materials with unique extremely fine-grained microstructures. The
systematic study of these materials showed the possibility of reaching homogeneous nano-grain microstructure
and high strength values exceeding 450 MPa in tension. Selected chemical composition and processing methods
led also to slightly decreased wear and corrosion rates and rather uniform corrosion. Keywords: zinc, mechanical alloying, biodegradable metals, composite, spark plasma sintering, extrusion, powder metallurgy Published in DiRROS: 23.07.2024; Views: 120; Downloads: 118
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33. A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmlandLorna J. Cole, David Kleijn, Lynn Dicks, Jane C. Stout, Simon G. Potts, Matthias Albrecht, Mario V. Balzan, Ignasi Bartomeus, Penelope J. Bebeli, Danilo Bevk, Jacobus C. Biesmeijer, Robert Chlebo, Anželika Dautarte, Nikolaos Emmanouil, Chris Hartfield, John M. Holland, Andrea Holzschuh, Nieke T. J. Knoben, Anikó Kovács-Hostyánszki, Yael Mandelik, Heleni Panou, Robert J. Paxton, Theodora Petanidou, Miguel A.A. Pinheiro de Carvalho, Maj Rundlöf, Jean-Pierre Sarthou, Menelaos C. Stavrinides, Maria Jose Suso, Hajnalka Szentgyörgyi, Bernard E. Vaissière, Androulla Varnava, Vilà Montserrat, Romualdas Zemeckis, Jeroen Scheper, 2020, original scientific article Abstract: Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in their potential to support insect pollinators under standard and pollinator-friendly management, as well as the extent of farmer uptake.
A structured Delphi elicitation process engaged 22 experts from 18 European countries to evaluate EFAs options. By considering life cycle requirements of key pollinating taxa (i.e. bumble bees, solitary bees and hoverflies), each option was evaluated for its potential to provide forage, bee nesting sites and hoverfly larval resources.
EFA options varied substantially in the resources they were perceived to provide and their effectiveness varied geographically and temporally. For example, field margins provide relatively good forage throughout the season in Southern and Eastern Europe but lacked early-season forage in Northern and Western Europe. Under standard management, no single EFA option achieved high scores across resource categories and a scarcity of late season forage was perceived.
Experts identified substantial opportunities to improve habitat quality by adopting pollinator-friendly management. Improving management alone was, however, unlikely to ensure that all pollinator resource requirements were met. Our analyses suggest that a combination of poor management, differences in the inherent pollinator habitat quality and uptake bias towards catch crops and nitrogen-fixing crops severely limit the potential of EFAs to support pollinators in European agricultural landscapes.
Policy Implications. To conserve pollinators and help protect pollination services, our expert elicitation highlights the need to create a variety of interconnected, well-managed habitats that complement each other in the resources they offer. To achieve this the Common Agricultural Policy post-2020 should take a holistic view to implementation that integrates the different delivery vehicles aimed at protecting biodiversity (e.g. enhanced conditionality, eco-schemes and agri-environment and climate measures). To improve habitat quality we recommend an effective monitoring framework with target-orientated indicators and to facilitate the spatial targeting of options collaboration between land managers should be incentivised. Keywords: agri-environment schemes, bees, CAP Green Architecture, Common Agricultural Policy, Ecological Focus Areas, habitat complementarity, pollination services, pollinator conservation Published in DiRROS: 22.07.2024; Views: 134; Downloads: 207
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34. One-step reverse-transcription digital PCR for reliable quantification of different pepino mosaic virus genotypesNataša Mehle, Larisa Gregur, Alexandra Bogožalec Košir, David Dobnik, 2020, original scientific article Abstract: 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. Keywords: digital PCR, pepino mosaic virus, quantification, genotype specific Published in DiRROS: 19.07.2024; Views: 142; Downloads: 56
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35. PLANiTS : a curated sequence reference dataset for plant ITS DNA metabarcodingElisa Banchi, Claudio Gennaro Ametrano, Samuele Greco, David Stanković, Lucia Muggia, Alberto Pallavicini, 2020, original scientific article Abstract: DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Keywords: DNA metabarcoding, reference datasets Published in DiRROS: 19.07.2024; Views: 137; Downloads: 89
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36. Feasibility of droplet digital PCR analysis of plasma cell-free DNA from kidney transplant patientsBarbara Jerič Kokelj, Maja Štalekar, Sebastian Vencken, David Dobnik, Polona Kogovšek, Matjaž Stanonik, Miha Arnol, Maja Ravnikar, 2021, original scientific article Abstract: Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patientsʼ plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA. Keywords: kidney transplantation, droplet digital PCR, plasma cell-free DNA, minor allele quantification, assay evaluation, graft health monitoring Published in DiRROS: 19.07.2024; Views: 131; Downloads: 66
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37. Sequestration of polystyrene microplastics by jellyfish mucusŽiva Lengar, Katja Klun, Iztok Dogša, Ana Rotter, David Stopar, 2021, original scientific article Abstract: The worldwide microplastics pollution is a serious environmental and health problem that is currently not effectively mitigated. In this work we tested jellyfish mucus as a new bioflocculent material capable of sequestration of polystyrene microplastics in aqueous environments. Mucus material was collected from different jellyfish species and was used to trap fluorescently tagged polystyrene microspheres. The efficiency of removal was tested using varying concentrations of microplastics and mucus. The interaction between the microplastics and mucus was determined by viscosity measurements and confocal laser scanning microscopy. Different mucus preparation methods were also tested: freshly prepared, mechanically sheared, freeze-thawed, freeze-dried, and hydrolyzed mucus. The results demonstrate that jellyfish mucus can efficiently sequester polystyrene microplastics particles from the suspension. The fraction of the removed microplastics was highest with freshly prepared mucus and decreased with freeze-thawing and freeze-drying. The mucus ability to sequester microplastics was completely lost in the hydrolyzed mucus. The results imply that the intact jellyfish mucus has the potential to be used as a biopolymer capable of removing microplastics material. Published in DiRROS: 19.07.2024; Views: 117; Downloads: 126
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38. Inactivation of pepper mild mottle virus in water by cold atmospheric plasmaArijana Filipić, David Dobnik, Magda Tušek-Žnidarič, Bojana Žegura, Alja Štern, Gregor Primc, Miran Mozetič, Maja Ravnikar, Jana Žel, Ion Gutiérrez-Aguirre, 2021, original scientific article Abstract: Water scarcity is one of the greatest threats for human survival and quality of life, and this is increasingly contributing to the risk of human, animal and plant infections due to waterborne viruses. Viruses are transmitted through polluted water, where they can survive and cause infections even at low concentrations. Plant viruses from the genus Tobamovirus are highly mechanically transmissible, and cause considerable damage to important crops, such as tomato. The release of infective tobamoviruses into environmental waters has been reported, with the consequent risk for arid regions, where these waters are used for irrigation. Virus inactivation in water is thus very important and cold atmospheric plasma (CAP) is emerging in this field as an efficient, safe, and sustainable alternative to classic waterborne virus inactivation methods. In the present study we evaluated CAP-mediated inactivation of pepper mild mottle virus (PMMoV) in water samples. PMMoV is a very resilient water-transmissible tobamovirus that can survive transit through the human digestive tract. The efficiency of PMMoV inactivation was characterized for infectivity and virion integrity, and at the genome level, using test plant infectivity assays, transmission electron microscopy, and molecular methods, respectively. Additionally, the safety of CAP treatment was determined by testing the cytotoxic and genotoxic properties of CAP-treated water on the HepG2 cell line. 5-min treatment with CAP was sufficient to inactivate PMMoV without introducing any cytotoxic or genotoxic effects in the in-vitro cell model system. These data on inactivation of such stable waterborne virus, PMMoV, will encourage further examination of CAP as an alternative for treatment of potable and irrigation waters, and even for other water sources, with emphasis on inactivation of various viruses including enteric viruses. Keywords: enteric viruses, pepper mild mottle virus, virus inactivation, water decontamination, cold atmospheric plasma Published in DiRROS: 19.07.2024; Views: 122; Downloads: 103
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39. Molecular systematics of the long-snouted deep water dogfish (Centrophoridae, Deania) with implications for identification, taxonomy, and conservationSergio Stefanni, Diana Catarino, Pedro A. Ribeiro, Mafalda Freitas, Gui Menezes, Francis Neat, David Stanković, 2021, original scientific article Abstract: According to the most recent taxonomical revision, the deep-sea dogfish genus Deania encompasses four species. Three of them, D. calcea, D. profundorum, and D. hystricosa, occur in the North Atlantic. Whilst D. profundorum can be identified by the presence of a subcaudal keel, the other two species are not easily visually distinguished. Uncertainties over identification raises concerns over stock units and whether management plans are adequate. In this study we compared onboard visual identification of Deania specimens, with morphological inspection of skin denticles under stereo microscope and with independent molecular taxonomical assignment using two molecular markers. Particular emphasis was paid to specimens identified as D. calcea and D. hystricosa in the NE Atlantic where these species potentially occur sympatrically and may be easily confused. In the past the species have been discriminated on the basis of the size of skin denticles (skin roughness), but our study showed that the crown length of skin denticles covaries with size (and sex), irrespective of species, and therefore this is not a reliable morphological character and should not be used to discriminate between the two species. Phylogenetic analyses did not indicate that D. hystricosa to be a distinct lineage from D. calcea. Interestingly, however four individuals (specimens from: UK, Azores Is., Madeira Is. and Seine seamount) formed a well-defined sub-clade nested within the D. calcea clade, possibly a signature of a past vicariance event or a result of coalescent stochasticity. Keywords: deep-sea sharks, fishery by-catch, phylogeny, Atlantic Ocean, deep-sea dogfish, skin denticles Published in DiRROS: 19.07.2024; Views: 133; Downloads: 83
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40. Controlling gene expression with deep generative design of regulatory DNAJan Zrimec, Xiaozhi Fu, Azam Sheikh Muhammad, Christos Skrekas, Vykintas Jauniskis, Nora K. Speicher, Christoph S. Börlin, Vilhelm Verendel, Morteza Haghir Chehreghani, Devdatt P. Dubhashi, Verena Siewers, Florian David Fitz, Jens Nielsen, Aleksej Zelezniak, 2022, original scientific article Abstract: Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Using mutagenesis typically requires screening sizable random DNA libraries, which limits the designs to span merely a short section of the promoter and restricts their control of gene expression. Here, we prototype a deep learning strategy based on generative adversarial networks (GAN) by learning directly from genomic and transcriptomic data. Our ExpressionGAN can traverse the entire regulatory sequence-expression landscape in a gene-specific manner, generating regulatory DNA with prespecified target mRNA levels spanning the whole gene regulatory structure including coding and adjacent non-coding regions. Despite high sequence divergence from natural DNA, in vivo measurements show that 57% of the highly-expressed synthetic sequences surpass the expression levels of highly-expressed natural controls. This demonstrates the applicability and relevance of deep generative design to expand our knowledge and control of gene expression regulation in any desired organism, condition or tissue. Published in DiRROS: 17.07.2024; Views: 264; Downloads: 119
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