1301. A small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensisAnja Pavlin, Anže Lovše, Gregor Bajc, Jan Otoničar, Amela Kujović, Živa Lengar, Ion Gutiérrez-Aguirre, Rok Kostanjšek, Janez Konc, Nadine Fornelos, Matej Butala, 2022, original scientific article Abstract: Bacillus thuringiensis serovar israelensis is the most widely used biopesticide against insects, including vectors of animal and human diseases. Among several extrachromosomal elements, this endospore-forming entomopathogen harbors two bacteriophages: a linear DNA replicon named GIL01 that does not integrate into the chromosome during lysogeny and a circular-jumbo prophage known as pBtic235. Here, we show that GIL01 hinders the induction of cohabiting prophage pBtic235. The GIL01-encoded small protein, gp7, which interacts with the host LexA repressor, is a global transcription regulator and represses the induction of pBtic235 after DNA damage to presumably allow GIL01 to multiply first. In a complex with host LexA in stressed cells, gp7 down-regulates the expression of more than 250 host and pBtic235 genes, many of which are involved in the cellular functions of genome maintenance, cell-wall transport, and membrane and protein stability. We show that gp7 homologs that are found exclusively in bacteriophages act in a similar fashion to enhance LexA’s binding to DNA, while likely also affecting host gene expression. Our results provide evidence that GIL01 influences both its host and its co-resident bacteriophage.
Published in DiRROS: 18.07.2024; Views: 283; Downloads: 224
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1302. Genome-informed design of a LAMP assay for the specific detection of the strain of ‘Candidatus Phytoplasma asteris’ phytoplasma occurring in grapevines in South AfricaŠpela Alič, Marina Dermastia, Johan Burger, Matthew Dickinson, Gerhard Pietersen, Gert Pietersen, Tanja Dreo, 2022, original scientific article Abstract: Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine ‘Candidatus Phytoplasma asteris’ that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.
Keywords: aster yellows, fruit, LAMP, molecular detection, pathogendetection, phytoplasma, Prokaryotes
Published in DiRROS: 17.07.2024; Views: 295; Downloads: 186
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1303. Where and how : new insight for brown algal forest restoration in the AdriaticMartina Orlando-Bonaca, Gilda Savonitto, Valentina Asnaghi, Domen Trkov, Valentina Pitacco, Milijan Šiško, Tihomir Makovec, Petra Slavinec, Ana Lokovšek, Saul Ciriaco, Mariachiara Chiantore, Sara Kaleb, Emmanuelle Patricia Descourvières, Marina Srijemsi, Annalisa Falace, 2022, original scientific article Abstract: Several anthropogenic factors are responsible for the decline of Cystoseira sensu lato (hereafter Cystoseira) forests along Mediterranean coasts. Some Cystoseira species are already regionally extinct, and their decline has been widely recorded. Sustainable and efficient techniques for the restoration of Cystoseira are needed. In this context, the objectives of this study were i) to analyse the reproductive traits of three populations of Gongolaria barbata from three nearby donor sites in the northern Adriatic Sea, assessing the differences in their reproductive potential and reproductive success; and ii) to evaluate the outplanting success in terms of the effectiveness of G. barbata restoration, in relation to the different donor and receiving sites (Miramare MPA and in front of the Marine Biology Station Piran - MBSP) and implemented methods (ex situ and hybrid method combining a mesocosm cultivation and a suspended culture in the field). After 2 weeks of cultivation in mesocosms, half of the tiles with germlings were transported to the receiving sites and placed on suspended lantern nets (hybrid method), which were later (after 3 months) transferred to the seabed on concrete plates with protective cages. The remaining tiles were placed on the seabed on concrete plates with protective cages after a 4-week culture (ex situ method). At both sites, lantern nets and plates were randomly placed at 3 m depth. Thallus length was measured monthly in each treatment. Seedlings in suspended culture showed lower performance at the Miramare MPA, most likely due to the unfavourable environmental conditions. The satisfactory results obtained at MBSP demonstrate the efficiency of the hybrid method and confirm its potential to reduce the cost and time required for cultivation. Since unpredictable climatic events pose the greatest threat to restoration performance, these challenges must be considered when establishing new restoration practices. Moreover, herbivore regulation is extremely urgent and should be planned and implemented on a larger regional scale.
Keywords: canopy-forming algae, restoration, ex situ, cultivation, Mediterranean Sea
Published in DiRROS: 17.07.2024; Views: 309; Downloads: 84
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1304. Assessment of different experimental setups to determineviral filtration efficiency of face masksArijana Filipić, Katja Fric, Maja Ravnikar, Polona Kogovšek, 2022, original scientific article Abstract: 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.
Keywords: face masks, virus filtration efficiency, bacterial filtration efficiency, EN 14683:2019+AC:2019, air sampler
Published in DiRROS: 17.07.2024; Views: 296; Downloads: 174
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1305. Trace metals and polycyclic aromatic hydrocarbons in the Eastern Mediterranean sediments : concentration ranges as a tool for quality control of large data collectionsMarina Lipizer, Branko Čermelj, 2022, original scientific article Abstract: Assessing the status of marine pollution at regional and sub-regional scales requires the use of comparable and harmonized data provided by multiple institutions, located in several countries. Standardized data management and quality control are crucial for supporting a coherent evaluation of marine pollution. Taking the Eastern Mediterranean Sea as a case study, we propose an approach to improve the quality control procedures used for sediment pollution data, thus supporting a harmonized environmental assessment. The regional ranges of contaminant concentrations in sediments were identified based on an in-depth literature review, and the lowest measured concentrations were evaluated to determine the “background concentrations” of chemical substances not yet targeted in the Mediterranean Sea. In addition, to verify the suitability of the approach for validating large data collections provided by multiple sources, the determined ranges were used to validate a regional dataset available through EMODnet data infrastructure.
Published in DiRROS: 17.07.2024; Views: 246; Downloads: 149
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1306. Soil water dynamics and olive yield (Olea europaea L.) under different surface drip irrigation treatments in northern MediterraneanMatic Noč, Urša Pečan, Marina Pintar, Maja Podgornik, 2024, original scientific article Abstract: The use of modern irrigation systems and monitoring of soil water status can help improve crop performance and water use efficiency. The influence of different irrigation treatments on soil water content dynamics and olive oil yield was studied over two growing seasons using a surface drip irrigation system in an olive grove in northern Mediterranean climate. Irrigation treatments included optimal irrigation, sustained deficit irrigation (33 % of optimal irrigation), and rainfed treatment. Based on the water applied, we calculated the percentage of replenished estimated evapotranspiration (ETc*) for each treatment using the Penman-Monteith method. Soil water content dynamics were monitored with capacitive probes at five depths (10 to 50 cm). The increase in soil water content at a depth of 30 to 50 cm, which was only achieved with optimal irrigation, resulted in a significantly higher olive oil yield. In contrast, deficit irrigation, despite the addition of water, did not lead to an increase in soil water in the layers below 30 cm, so that the yield was equal to that of rainfed treatment. In irrigated olive groves, it is beneficial to monitor the water content of the soil at several depths to ensure that a sufficient amount of water has been applied.Uporaba sodobnih namakalnih sistemov ter spremljanje stanja vode v tleh lahko pripomore k izboljšanju učinkovitosti rastlinske pridelave in rabe vode. Vpliv različnih načinov namakanja na dinamiko vsebnosti vode v tleh in pri-delek oljčnega olja smo preučevali v dveh rastnih dobah z upo-rabo površinskega kapljičnega namakalnega sistema v oljčnem nasadu v severnem sredozemskem podnebju. Obravnavanja so vključevala optimalno namakanje, trajno namakanje s priman-jkljajem (33 % optimalnega namakanja) in brez namakanja. Na podlagi porabljene vode smo z uporabo metode Penman-Mon-teith izračunali odstotek nadomeščene ocenjene evapotranspi-racije (ETc*) za vsako obravnavo. Dinamiko vsebnosti vode v tleh smo spremljali s kapacitivnimi merilniki na petih globinah (od 10 do 50 cm). Povečanje vsebnosti vode v tleh na globini od 30 do 50 cm, ki je bilo doseženo le z optimalnim namakanjem, je povzročilo večji pridelek oljčnega olja. Nasprotno pa se pri namakanju s primanjkljajem kljub dodajanju vode ni povečala količina vode v tleh v plasteh pod 30 cm, zato je bil pridelek enak pridelku brez namakanja. V namakanih oljčnih nasadih je koristno spremljati vsebnost vode v tleh na več globinah, da se zagotovi, da je bila priskrbljena zadostna količina vode
Keywords: diviner, evapotranspiration, irrigation management, olive, soil depths, volumetric soil water content
Published in DiRROS: 17.07.2024; Views: 256; Downloads: 270
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1307. Learning deep representations of enzyme thermal adaptationGang Li, Filip Buric, Jan Zrimec, Sandra Viknander, Jens Nielsen, Aleksej Zelezniak, Martin K. M. Engqvist, 2022, original scientific article Abstract: Temperature is a fundamental environmental factor that shapes the evolution of organisms. Learning thermal determinants of protein sequences in evolution thus has profound significance for basic biology, drug discovery, and protein engineering. Here, we use a data set of over 3 million BRENDA enzymes labeled with optimal growth temperatures (OGTs) of their source organisms to train a deep neural network model (DeepET). The protein-temperature representations learned by DeepET provide a temperature-related statistical summary of protein sequences and capture structural properties that affect thermal stability. For prediction of enzyme optimal catalytic temperatures and protein melting temperatures via a transfer learning approach, our DeepET model outperforms classical regression models trained on rationally designed features and other deep-learning-based representations. DeepET thus holds promise for understanding enzyme thermal adaptation and guiding the engineering of thermostable enzymes.
Keywords: bioinformatics, deep neural networks, enzyme catalytic temperatures, optimal growth temperatures, protein thermostability, transfer learning
Published in DiRROS: 17.07.2024; Views: 318; Downloads: 212
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1308. Optimization of a calcium-based treatment method for jellyfish to design food for the futureFrancesca Anna Ramires, Stefania De Domenico, Danilo Migoni, Francesco Paolo Fanizzi, Dror Angel, Rasa Slizyte, Katja Klun, Gianluca Bleve, Antonella Leone, 2022, original scientific article Abstract: 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.
Keywords: jellyfish, novel food, safety, quality, nutritional traits, organic calcium salts
Published in DiRROS: 17.07.2024; Views: 289; Downloads: 208
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1309. Long-term ringing data on migrating passerines reveal overall avian decline in EuropeTina Petras, Al Vrezec, 2022, original scientific article Abstract: The loss of biodiversity is shaping today’s environment. Bird ringing is a citizen science research tool that can determine species population dynamics and trends over a large geographic area. We used a 17-year time series to assess population trends of 74 passerine species based on ringing data from autumn migration in Slovenia (south-central Europe). We defined seven guilds of species according to geographic location, ecological, migratory, breeding, and life-history traits. Almost all guilds showed declining trends, except for the group of species of northeastern European origin, which showed a stable trend. The greatest decline was in low-productivity wetland specialists. Forest birds, seed-eaters, and high-productivity species experienced the smallest declines. The general declines in avifauna across a range of life-history and behavioural traits, and across a range of spatial and ecological scales, suggest widespread environmental change in Europe. Our data indicates that recent trends are toward ecosystem homogeneity, with an impoverished avifauna, including a few species that are increasing in abundance. These are the species with higher productivity and flexible behaviour, such as short-distance migrants, that have the greatest chance of prevailing in the recently rapidly changing environment because of their ability to adapt to changes in a timely manner.
Keywords: bird population trends, ecological traits, life-history traits, migratory traits, recovery analysis, avifaunal change
Published in DiRROS: 17.07.2024; Views: 288; Downloads: 210
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1310. Transcriptional deregulation of stress-growth balance in Nicotiana benthamiana biofactories producing insect sex pheromonesMojca Juteršek, Marko Petek, Živa Ramšak, Elena Moreno Gimenéz, Silvia Gianoglio, Rubèn Mateos Fernández, Diego Orzaez, Kristina Gruden, Špela Baebler, 2022, original scientific article Abstract: Plant biofactories are a promising platform for sustainable production of high-value compounds, among which are insect sex pheromones, a green alternative to conventional insecticides in agriculture. Recently, we have constructed transgenic Nicotiana benthamiana plants (“Sexy Plants”, SxP) that successfully produce a blend of moth (Lepidoptera) sex pheromone compounds (Z)-11-hexadecen-1-ol and (Z)-11-hexadecenyl acetate. However, efficient biosynthesis of sex pheromones resulted in growth and developmental penalty, diminishing the potential for commercial use of SxP in biomanufacturing. To gain insight into the underlying molecular responses, we analysed the whole-genome transcriptome and evaluated it in relation to growth and pheromone production in low- and high-producing transgenic plants of v1.0 and v1.2 SxP lines. In our study, high-producing SxPv1.2 plants accumulated the highest amounts of pheromones but still maintained better growth compared to v1.0 high producers. For an in-depth biological interpretation of the transcriptomic data, we have prepared a comprehensive functional N. benthamiana genome annotation as well as gene translations to Arabidopsis thaliana, enabling functional information transfer by using Arabidopsis knowledge networks. Differential gene expression analysis, contrasting pheromone producers to wild-type plants, revealed that while only a few genes were differentially regulated in low-producing plants, high-producing plants exhibited vast transcriptional reprogramming. They showed signs of stress-like response, manifested as downregulation of photosynthesis-related genes and significant differences in expression of hormonal signalling and secondary metabolism-related genes, the latter presumably leading to previously reported volatilome changes. Further network analyses confirmed stress-like response with activation of jasmonic acid and downregulation of gibberellic acid signalling, illuminating the possibility that the observed growth penalty was not solely a consequence of a higher metabolic burden imposed upon constitutive expression of a heterologous biosynthetic pathway, but rather the result of signalling pathway perturbation. Our work presents an example of comprehensive transcriptomic analyses of disadvantageous stress signalling in N. benthamiana biofactory that could be applied to other bioproduction systems.
Keywords: transcriptomics, plant biotechnology, jasmonic acid, growthstress tradeoffs, network analysis, growth penalty, insect sex pheromone
Published in DiRROS: 17.07.2024; Views: 351; Downloads: 208
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