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41.
Assessment of different experimental setups to determineviral filtration efficiency of face masks
Arijana Filipić, Katja Fric, Maja Ravnikar, Polona Kogovšek, 2022, izvirni znanstveni članek

Povzetek: Abstract As a result of the COVID-19 pandemic, many new materials and masks came onto the market. To determine their suitability, several standards specify which properties to test, including bacterial filtration efficiency (BFE), while none describe how to determine viral filtration efficiency (VFE), a property that is particularly important in times of pandemic. Therefore, we focused our research on evaluating the suitability and efficiency of different systems for determining VFE. Here, we evaluated the VFE of 6 mask types (e.g., a surgical mask, a respirator, material for mask production, and cloth masks) with different filtration efficiencies in four experimental setups and compared the results with BFE results. The study included 17 BFE and 22 VFE experiments with 73 and 81 mask samples tested, respectively. We have shown that the masks tested had high VFE (>99% for surgical masks and respirators, ≥98% for material, and 87–97% for cloth masks) and that all experimental setups provided highly reproducible and reliable VFE results (coefficient of variation < 6%). Therefore, the VFE tests described in this study can be integrated into existing standards for mask testing.
Ključne besede: face masks, virus filtration efficiency, bacterial filtration efficiency, EN 14683:2019+AC:2019, air sampler
Objavljeno v DiRROS: 17.07.2024; Ogledov: 227; Prenosov: 137
.pdf Celotno besedilo (1,17 MB)
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42.
Optimization of a calcium-based treatment method for jellyfish to design food for the future
Francesca Anna Ramires, Stefania De Domenico, Danilo Migoni, Francesco Paolo Fanizzi, Dror Angel, Rasa Slizyte, Katja Klun, Gianluca Bleve, Antonella Leone, 2022, izvirni znanstveni članek

Povzetek: Edible jellyfish are a traditional Southeast Asian food, usually prepared as a rehydrated product using a salt and alum mixture, whereas they are uncommon in Western Countries and considered as a novel food in Europe. Here, a recently developed, new approach for jellyfish processing and stabilization with calcium salt brining was upgraded by modifying the pre-treatment step of freshly caught jellyfish and successfully applied to several edible species. Treated jellyfish obtained by the application of the optimized version of this method respected both quality and safety parameters set by EU law, including no pathogenic microorganisms, absence or negligible levels of histamine and of total volatile basic nitrogen, no heavy metals; and the total bacterial, yeast, and mold counts were either negligible or undetectable. Jellyfish treated by the presented method exhibited unique protein content, amino acid and fatty acid profiles, antioxidant activity, and texture. The optimized method, initially set up on Rhiszostoma pulmo, was also successfully applied to other edible jellyfish species (such as Cotylorhiza tuberculata, Phyllorhiza punctata, and Rhopilema nomadica) present in the Mediterranean Sea. This study discloses an innovative process for the preparation of jellyfish-based food products for potential future distribution in Europe.
Ključne besede: jellyfish, novel food, safety, quality, nutritional traits, organic calcium salts
Objavljeno v DiRROS: 17.07.2024; Ogledov: 214; Prenosov: 152
.pdf Celotno besedilo (1,11 MB)
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43.
CRISPR/Cas9-mediated fine-tuning of miRNA expression in tetraploid potato
Tjaša Lukan, Florian Veillet, Maja Križnik, Anna Coll Rius, Tjaša Mahkovec Povalej, Karmen Pogačar, Katja Stare, Laura Chauvin, Jean-Eric Chauvin, Kristina Gruden, 2022, izvirni znanstveni članek

Povzetek: MicroRNAs (miRNAs) are small noncoding RNAs, which modulate the abundance and spatiotemporal accumulation of target mRNAs at transcriptional and post-transcriptional levels and through that play important roles in several biological processes in plants. Here we show that in polyploid species, CRISPR/Cas9 system can be used for fine-tuning of miRNA expression, which can have broader range of applications compared to knock-out mutants. We established the complete pipeline for CRISPR-Cas9-mediated modulation of miRNA expression in potato. It consists of (1) design and assembly of dual sgRNA CRISPR/Cas9 constructs, (2) transient transfection of protoplasts following fast and efficient screening by high resolution melting analysis to select functional sgRNAs, and (3) stable transformation of potato explants with functional sgRNAs and selection of regenerated transgenic lines with desired mutations and desired miRNA abundance based on sequencing and RT-qPCR. We show that miRNA-editing using dual sgRNA approach results in different types of mutations among transgenic lines but also in different alleles of the same plant, which are target site-dependent. The most frequent were short deletions, but we also detected 1-nt insertions (T or G), deletions between two sgRNAs and larger deletions. miRNA abundance correlates with the frequency and type of introduced mutations, as more extensive mutations in more alleles result in lower miRNA abundance. Interestingly, some mutated loci can generate alternative miRNAs, now novel targets were however predicted for those. In all transgenic lines with Cas9 expression, we detected mutations, suggesting high efficiency of Cas9-editing. We confirmed the miRNA-editing efficiency of our optimised approach in two different potato genotypes and three different loci.
Ključne besede: CRISPR/Cas9, hypersensitive response (HR)-conferred resistance, immune signaling, live cell imaging, Solanum tuberosum (potato), spatiotemporal analysis, stromules, virus resistance
Objavljeno v DiRROS: 17.07.2024; Ogledov: 243; Prenosov: 189
.pdf Celotno besedilo (2,94 MB)
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44.
Diversity of molluscan assemblage in relation to biotic and abiotic variables in brown algal forests
Martina Orlando-Bonaca, Domen Trkov, Katja Klun, Valentina Pitacco, 2022, izvirni znanstveni članek

Povzetek: Canopy-forming macroalgae, mainly those belonging to the order Fucales, form the so-called brown algal forests, which are among the most productive assemblages in shallow coastal zones. Their vertical, branching canopies increase nearshore primary production, provide nursery areas for juvenile fish, and sustain understory assemblages of smaller algae and both sessile and vagile fauna. The majority of benthic invertebrates inhabiting these forests have larval stages that spend some time floating freely or swimming in the plankton. Therefore, canopy-forming macroalgae play an important role as species collectors related to larval supply and hydrodynamic processes. During the past several decades, brown algal forests have significantly reduced their extension and coverage in the Mediterranean basin, due to multiple interacting natural and anthropogenic pressures, with negative consequences also for the related fauna. The aim of this research was to examine how differences in macrophyte abundance and structure, as well as environmental variables, affect the associated molluscan communities in the shallow northern Adriatic Sea. Sampling sites with well-developed vegetation cover dominated by different canopy-forming species were selected in the shallow infralittoral belt of the northern Adriatic Sea in the spring–summer period of the years 2019 and 2020. Our results confirm the importance of algal forests for molluscan assemblage, with a total of 68 taxa of molluscs found associated with macrophytes. Gastropods showed the highest richness and abundance, followed by bivalves. Mollusc richness and diversity (in terms of biotic indices) were not related with the degree of development of canopy-forming species (in terms of total cover and total volume), nor with the ecological status of benthic macroalgae at different depths. On the contrary, the variability in molluscan taxa abundances was explained by some environmental variables, such as temperature, pH, light, and nitrates concentration.
Ključne besede: canopy-forming algae, coverage, molluscan assemblage, diversity, abiotic factors, Adriatic Sea
Objavljeno v DiRROS: 17.07.2024; Ogledov: 180; Prenosov: 176
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45.
Fermentative indole production via bacterial tryptophan synthase alpha subunit and plant indole-3-glycerol phosphate lyase enzymes
Lenny Ferrer, Melanie Mindt, Maria Suarez-Diez, Tatjana Jilg, Maja Zagorščak, Jin-Ho Lee, Kristina Gruden, Volker F. Wendisch, Katarina Cankar, 2022, izvirni znanstveni članek

Povzetek: Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol phosphate (IGP) by plant indole-3-glycerol phosphate lyases (IGLs). While it is widely accepted that the tryptophan synthase α-subunit (TSA) has intrinsically low IGL activity in the absence of the tryptophan synthase β-subunit, in this study, we show that Corynebacterium glutamicum TSA functions as a bona fide IGL and can support fermentative indole production in strains providing IGP. By bioprospecting additional bacterial TSAs and plant IGLs that function as bona fide IGLs were identified. Capturing indole in an overlay enabled indole production to titers of about 0.7 g L–1 in fermentations using C. glutamicum strains expressing either the endogenous TSA gene or the IGL gene from wheat.
Ključne besede: Corynebacterium glutamicum, indole, indole-3-glycerol phosphate lyase, tryptophan synthase α-subunit, bioprospecting, fermentative production
Objavljeno v DiRROS: 16.07.2024; Ogledov: 232; Prenosov: 185
.pdf Celotno besedilo (2,24 MB)
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46.
Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the ocean
Mario Pinto, Zihao Zhao, Katja Klun, Eugen Libowitzky, Gerhard J. Herndl, 2022, izvirni znanstveni članek

Povzetek: Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analyzed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for 2 years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harbored genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase, respectively. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This report identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential for utilizing LDPE-associated compounds as carbon and energy source. IMPORTANCE Low-density polyethylene (LDPE) is one of the most used plastics worldwide, and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements, and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After 2 years of incubation, two of the microbial communities exhibited very similar taxonomic compositions mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean that might have the potential to degrade LDPE-associated compounds and that alkane degradation pathways might be involved.
Ključne besede: LDPE, ocean, biodegradation, biofilms, metagenomics
Objavljeno v DiRROS: 16.07.2024; Ogledov: 312; Prenosov: 163
.pdf Celotno besedilo (6,01 MB)
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47.
Fast assay to predict multipotent mesenchymal stromal cell replicative senescence dynamics
Katja Kološa, Aleš Leskovšek, Teja Rajar, Tamara Lah Turnšek, 2022, izvirni znanstveni članek

Povzetek: The major obstacle to the application of mesenchymal stromal cells (MSCs) in regenerative medicine is the expansion of the donor-derived cells in vitro to obtain high cell numbers in the shortest possible time. However, MSCs gradually undergo replicative senescence after a variable number of divisions that reduce their therapeutic efficacy, which needs to be determined before administration. The authors developed a fast and simple evaluation assay testing two senescence inducers, mitoxantrone (Mxt) and trichostatin A (TSA), to predict the onset of spontaneous replicative senescence of adipose-derived mesenchymal stromal cells (ASCs) and have confirmed the correlation between induced senescence and spontaneous replicative senescence in the assay using Mxt. This protocol facilitates the standardization of therapeutic ASCs and MSCs from other origins before application.
Ključne besede: adipose mesenchymal stromal (stem) cells (ASCs), cell longevity, induced senescence, mesenchymal stromal (stem) cells (MSCs), mitoxantrone, replicative senescence, trichostatin A
Objavljeno v DiRROS: 16.07.2024; Ogledov: 200; Prenosov: 110
.pdf Celotno besedilo (1,19 MB)
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48.
Evaluation of soluble mesothelin-related peptides and MSLN genetic variability in asbestos-related diseases
Katja Goričar, Viljem Kovač, Metoda Dodič-Fikfak, Vita Dolžan, Alenka Franko, 2020, izvirni znanstveni članek

Povzetek: Background Asbestos exposure is associated with increased risk of several diseases, including malignant mesothelioma (MM). Cell surface glycoprotein mesothelin is overexpressed in MM and serum soluble mesothelin-related peptides (SMRP) were already proposed as a diagnostic or prognostic biomarker in MM. However, interindividual variability in serum SMRP levels limits the clinical usefulness. Our primary objective was to investigate the influence of MSLN rs1057147 on serum SMRP levels in asbestos-exposed subjects and patients with asbestos-related diseases as well as on survival in MM. Subjects and methods Among 782 asbestos-exposed subjects and patients with asbestos-related diseases, 154 had MM. Serum SMRP levels were determined using sandwich enzyme-linked immunosorbent assay. All subjects were genotyped for MSLN rs1057147 polymorphism using competitive allele-specific polymerase chain reaction. Nonparametric tests, logistic and Cox regression were used in statistical analysis to compare different subject groups. Results MM patients had significantly higher SMRP levels than all other subjects (p < 0.001). Compared to wild-type MSLN rs1057147 genotype, both heterozygotes and carriers of two polymorphic alleles had significantly higher SMRP levels among subjects without MM (p < 0.001), but not in MM patients (p = 0.424). If genotype information was included, specificity of SMRP increased from 88.5% to 92.7% for the optimal cutoff value. Overall survival was significantly shorter in MM patients carrying at least one polymorphic rs1057147 allele (HR = 1.72, 95% CI = 1.15-2.55, p = 0.008). Conclusions MSLN genetic variability affects serum SMRP levels and was associated with shorter survival of MM patients. Combination of genetic and serum factors could therefore serve as a better diagnostic or prognostic biomarker in MM patients.
Ključne besede: asbestos-related disease, malignant mesothelioma, mesothelin
Objavljeno v DiRROS: 16.07.2024; Ogledov: 206; Prenosov: 122
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49.
The influence of genetic variability in IL1B and MIR146A on the risk of pleural plaques and malignant mesothelioma
Petra Piber, Neža Vavpetič, Katja Goričar, Vita Dolžan, Viljem Kovač, Alenka Franko, 2020, izvirni znanstveni članek

Povzetek: Asbestos exposure is associated with the development of pleural plaques as well as malignant mesothelioma (MM). Asbestos fibres activate macrophages, leading to the release of inflammatory mediators including interleukin 1 beta (IL-1%). The expression of IL-1% may be influenced by genetic variability of IL1B gene or regulatory microRNAs (miRNAs). This study investigated the effect of polymorphisms in IL1B and MIR146A genes on the risk of developing pleural plaques and MM. Subjects and methods. In total, 394 patients with pleural plaques, 277 patients with MM, and 175 healthy control subjects were genotyped for IL1B and MIR146A polymorphisms. Logistic regression was used in statistical analysis. Results. We found no association between MIR146A and IL1B genotypes, and the risk of pleural plaques. MIR146A rs2910164 was significantly associated with a decreased risk of MM (OR = 0.31, 95% CI = 0.13%0.73, p = 0.008). Carriers of two polymorphic alleles had a lower risk of developing MM, even after adjustment for gender and age (OR = 0.34, 95% CI = 0.14%0.85, p = 0.020). Among patients with known asbestos exposure, carriers of at least one polymorphic IL1B rs1143623 allele also had a lower risk of MM in multivariable analysis (OR = 0.50, 95% CI = 0.28%0.92, p = 0.025). The interaction between IL1B rs1143623 and IL1B rs1071676 was significantly associated with an increased risk of MM (p = 0.050). Conclusions. Our findings suggest that genetic variability of inflammatory mediator IL-1% could contribute to the risk of developing MM, but not pleural plaques.
Ključne besede: asbestos, genetic variation, malignant mesothelioma, pleural plaques
Objavljeno v DiRROS: 16.07.2024; Ogledov: 229; Prenosov: 58
.pdf Celotno besedilo (327,61 KB)

50.
Bacterial indicators are ubiquitous members of pelagic microbiome in anthropogenically impacted coastal ecosystem
Neža Orel, Eduard Fadeev, Katja Klun, Matjaž Ličer, Tinkara Tinta, Valentina Turk, 2022, izvirni znanstveni članek

Povzetek: Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.
Objavljeno v DiRROS: 16.07.2024; Ogledov: 223; Prenosov: 154
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