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1582. 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: 505; Downloads: 224
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1583. Diversity of molluscan assemblage in relation to biotic and abiotic variables in brown algal forestsMartina Orlando-Bonaca, Domen Trkov, Katja Klun, Valentina Pitacco, 2022, original scientific article Abstract: 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.
Keywords: canopy-forming algae, coverage, molluscan assemblage, diversity, abiotic factors, Adriatic Sea
Published in DiRROS: 17.07.2024; Views: 317; Downloads: 237
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1584. |
1585. An insight into the feeding ecology of Serranus Scriba, a Shallow water mesopredator in the Northern Adriatic Sea, with a non-destructive methodAna Lokovšek, Martina Orlando-Bonaca, Domen Trkov, Lovrenc Lipej, 2022, original scientific article Abstract: Serranus scriba is a common member of the coastal fish community in the Adriatic Sea, but knowledge about its feeding ecology is scarce. The aim of this paper is to present new evidence about its food preferences and feeding habits. An innovative non-destructive method of fecal pellet analysis was used for this study. This method does not require sacrificing specimens and the fish can be released back into the sea alive after the laboratory work. The results demonstrated that S. scriba mainly preys on decapods, followed by polychaetes, isopods, fish, mollusks and swarming shrimps. The calculated index of trophic diversity (ITD) value of 0.89 indicates that it is an opportunistic feeder that feeds on a wide range of different prey. According to the calculated trophic level of 3.43, which is higher than that of other members of the community, S. scriba is also an important piscivorous predator. With age, S. scriba undergoes an ontogenetic shift. The proportion of crustaceans, gastropods and polychaetes decreases with age and body size, while the proportion of fish increases.
Keywords: coastal fishes, diet, non-destructive method, non-lethal method, painted comber, northern Adriatic
Published in DiRROS: 17.07.2024; Views: 337; Downloads: 194
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1586. Evaluation of methods and processes for robust monitoring of SARS-CoV-2 in wastewaterOlivera Maksimović, Živa Lengar, Zala Kogej Zwitter, Katarina Bačnik, Irena Bajde, Mojca Milavec, Anže Županič, Nataša Mehle, Denis Kutnjak, Maja Ravnikar, Ion Gutiérrez-Aguirre, 2022, original scientific article Abstract: The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
Keywords: waste water, method evolution, virus detection, SARS-CoV-2
Published in DiRROS: 17.07.2024; Views: 332; Downloads: 213
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1587. What did we achieve with VALITEST an EU project on validation in plant pest diagnostics?Charlotte Trontin, Barbara Agstner, Denise Altenbach, Géraldine Anthoine, Hanna Baginska, Ian Brittain, A Chabirand, Anne-Marie Chappé, P. Dahlin, Tanja Dreo, C. Freye-Minks, Camilo Gianinazzi, Catherine Harrison, Glyn Jones, Marco Stefan Kaiser, Marta Luigi, Sébastien Massart, Nataša Mehle, Monica Mezzalama, Hanna Mouaziz, Maja Ravnikar, Tom Raaymakers, Jean-Philippe Renvoise, Mathieu Rolland, Marta Santos, Sam Seddas, René van der Vlugt, Ana Vučurović, Françoise Petter, 2022, original scientific article Keywords: plant pest diagnostics, validation, test performance study, high-throughput, sequencing, reference material, training
Published in DiRROS: 17.07.2024; Views: 403; Downloads: 195
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1588. Tartary buckwheat flavonoids improve colon lesions and modulate gut microbiota composition in diabetic miceWenwen Cheng, Cifeng Cai, Ivan Kreft, Tamara Lah Turnšek, Mingyan Zu, Yongping Hu, Meiliang Zhou, Zhiyong Liao, 2022, original scientific article Abstract: Tartary buckwheat flavonoids (TBFs) exhibit diverse biological activities, with antioxidant, antidiabetes, anti-inflammatory, and cholesterol-lowering properties. In this study, we investigated the role of TBFs in attenuating glucose and lipid disturbances in diabetic mice and hence preventing the occurrence of diabetes-related colon lesions in mice by regulating the gut microbiota. The results showed that TBFs (1) reversed blood glucose levels and body weight changes; (2) improved levels of serum total cholesterol (TC), triglycerides (TGs), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and fasting insulin; and (3) significantly reduced diabetes-related colon lesions in diabetic mice. In addition, TBFs also affected the diabetes-related imbalance of the gut microbiota and enriched beneficial microbiota, including Akkermansia and Prevotella. The TBF also selectively increased short-chain fatty acid-producing bacteria, including Roseburia and Odoribacter, and decreased the abundance of the diabetes-related gut microbiota, including Escherichia, Mucispirillum, and Bilophila. The correlation analysis indicated that TBFs improved metabolic parameters related to key communities of the gut microbiota. Our data suggested that TBFs alleviated glucose and lipid disturbances and improved colon lesions in diabetic mice, possibly by regulating the community composition of the gut microbiota. This regulation of the gut microbiota composition may explain the observed effects of TBFs to alleviate diabetes-related symptoms.
Keywords: Tartary buckwheat, flavonoids, microbiota, mice
Published in DiRROS: 17.07.2024; Views: 274; Downloads: 272
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1589. Biological and genetic characterization of Physostegia chlorotic mottle virus in Europe based on host range, location, and timeColine Temple, Arnaud G. Blouin, Kris De Jonghe, Yoika Foucart, Marleen Botermans, Marcel Westenberg, Ruben Schoen, Pascal Gentit, Michèle Visage, Eric Verdin, Mark Paul Selda Rivarez, Denis Kutnjak, Ana Vučurović, 2022, original scientific article Abstract: Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.
Published in DiRROS: 17.07.2024; Views: 468; Downloads: 219
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1590. Natural analogues in pH variability and predictability across the coastal pacific estuaries : extrapolation of the increased oyster dissolution under increased ph amplitude and low predictability related to ocean acidificationNina Bednaršek, Marcus W. Beck, Greg Pelletier, Scott Lee Applebaum, Richard Alan Feely, Robert Butler, Maria Byrne, Betsy Peabody, Jonathan Davis, Jasna Štrus, 2022, original scientific article Abstract: Coastal-estuarine habitats are rapidly changing due to global climate change, with impacts influenced by the variability of carbonate chemistry conditions. However, our understanding of the responses of ecologically and economically important calcifiers to pH variability and temporal variation is limited, particularly with respect to shell-building processes. We investigated the mechanisms driving biomineralogical and physiological responses in juveniles of introduced (Pacific; Crassostrea gigas) and native (Olympia; Ostrea lurida) oysters under flow-through experimental conditions over a six-week period that simulate current and future conditions: static control and low pH (8.0 and 7.7); low pH with fluctuating (24-h) amplitude (7.7 ± 0.2 and 7.7 ± 0.5); and high-frequency (12-h) fluctuating (8.0 ± 0.2) treatment. The oysters showed physiological tolerance in vital processes, including calcification, respiration, clearance, and survival. However, shell dissolution significantly increased with larger amplitudes of pH variability compared to static pH conditions, attributable to the longer cumulative exposure to lower pH conditions, with the dissolution threshold of pH 7.7 with 0.2 amplitude. Moreover, the high-frequency treatment triggered significantly greater dissolution, likely because of the oyster’s inability to respond to the unpredictable frequency of variations. The experimental findings were extrapolated to provide context for conditions existing in several Pacific coastal estuaries, with time series analyses demonstrating unique signatures of pH predictability and variability in these habitats, indicating potentially benefiting effects on fitness in these habitats. These implications are crucial for evaluating the suitability of coastal habitats for aquaculture, adaptation, and carbon dioxide removal strategies.
Keywords: ocean acidification, diel pH variability, amplitude, shell dissolution, predictability
Published in DiRROS: 17.07.2024; Views: 333; Downloads: 306
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