711. The importance of jellyfish-microbe interactions for biogeochemical cycles in the oceanTinkara Tinta, Katja Klun, Gerhard J. Herndl, 2021, review article Abstract: Jellyfish blooms can represent a significant but largely overlooked source of organic matter (OM), in particular at the local and regional scale. We provide an overview of the current state of knowledge on the bloom-forming jellyfish as sink and source of OM for microorganisms. In particularly, we compare the composition, concentration, and release rates of the OM excreted by living jellyfish with the OM stored within jellyfish biomass, which becomes available to the ocean's interior only once jellyfish decay. We discuss how these two stoichiometrically different jelly-OM pools might influence the dynamics of microbial community and the surrounding ecosystem. We conceptualize routes of jelly-OM in the ocean, focusing on different envisioned fates of detrital jelly-OM. In this conceptual framework, we revise possible interactions between different jelly-OM pools and microbes and highlight major knowledge gaps to be addressed in the future.
Published in DiRROS: 05.08.2024; Views: 288; Downloads: 224
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712. A primer on the analysis of high-throughput sequencing data for detection of plant virusesDenis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan F. Kreuze, Marie Lefebvre, Goncalo Silva, Martha Malapi-Wight, Paolo Margaria, Irena Mavrič Pleško, Sam McGreig, Laura Miozzi, Benoit Remenant, Jean-Sébastien Reynard, Johan Rollin, Mike Rott, Olivier Schumpp, Sébastien Massart, Annelies Haegeman, 2021, review article Abstract: High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
Keywords: plant virus, high-throughput sequencing, bioinformatics, detection, discovery
Published in DiRROS: 05.08.2024; Views: 295; Downloads: 252
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713. Response of hyporheic biofilms to temperature changes and dissolved organic carbon enrichment: a mesocosm study : a mesocosm studyTatjana Simčič, Monika Poklukar, Nataša Mori, 2023, original scientific article Abstract: Purpose
Hyporheic biofilms are the central site for biogeochemical cycling in streams and rivers. In view of global warming and increasing human pressures, this study aimed to compare the response of hyporheic biofilm biomass and activities from an unpolluted reference stream reach surrounded by forest with those from a stream reach exposed to agricultural and urban land use using a mesocosm experiment in which the water temperature and dissolved organic carbon (DOC) contents were manipulated.
Methods
Hyporheic sediments collected in the field from the two study reaches (i.e. reference and impacted) were incubated in the laboratory at two different temperatures (10 °C, 14 °C) and wetted with three types of synthetic water (control [C] – 0 mg L−1; low DOC – 5 mg L−1; high DOC – 30 mg L−1) for four weeks. The responses of the hyporheic biofilms were measured weekly using structural (total protein content [TPC] as a proxy for biofilm biomass) and functional measures (electron transport system activity [ETSA] and community-level physiological profiling [CLPP]).
Results
The response of hyporheic biofilms to temperature changes and DOC enrichment was site-specific for all studied measures (TPC, ETSA and CLPP, including measured average well colour development [AWCD]). The addition of DOC to biofilms from the pristine stream reach significantly heightened the responses at 10 °C, a temperature within the normal environmental temperature ranges of the reference location, but not at 14 °C, which was here, a temperature outside normal environmental range. On the other hand, biofilms from the impacted stream reach exhibited increased responses following DOC enrichment under both temperature regimes, with a particularly pronounced response at 14 ºC, in this case, both experimental temperatures were within the normal environmental temperature ranges of the study locations.
Conclusion
Hyporheic biofilms were shown to be, like benthic biofilms, sensitive to temperature changes and organic enrichment, but their response to temperature changes and enrichment caused by climate change and/or other anthropogenic pressures (i.e. point and non-point pollution, removal of the riparian zone, hydromorphological modifications, etc.) was not simply linear but site-specific. The intensity of the response, characterized by increased activity and biomass production, appears to be constrained within the temperature ranges prevalent in the environment from which the biofilms originate. These findings emphasize the importance of site-specific considerations in predicting the impacts of climate change and anthropogenic pressures on these critical components of river and stream ecosystems.
Keywords: sediments, respiration, enzymes, functional indicators, interactions
Published in DiRROS: 05.08.2024; Views: 298; Downloads: 254
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714. Energy metabolism in IDH1 wild-type and IDH1-mutated glioblastoma stem cells : a novel target for therapy?Cornelis J. F. van Noorden, Vashendriya V. V. Hira, Amber J. van Dijck, Metka Novak, Barbara Breznik, Remco J. Molenaar, 2021, review article Abstract: Cancer is a redox disease. Low levels of reactive oxygen species (ROS) are beneficial for cells and have anti-cancer effects. ROS are produced in the mitochondria during ATP production by oxidative phosphorylation (OXPHOS). In the present review, we describe ATP production in primary brain tumors, glioblastoma, in relation to ROS production. Differentiated glioblastoma cells mainly use glycolysis for ATP production (aerobic glycolysis) without ROS production, whereas glioblastoma stem cells (GSCs) in hypoxic periarteriolar niches use OXPHOS for ATP and ROS production, which is modest because of the hypoxia and quiescence of GSCs. In a significant proportion of glioblastoma, isocitrate dehydrogenase 1 (IDH1) is mutated, causing metabolic rewiring, and all cancer cells use OXPHOS for ATP and ROS production. Systemic therapeutic inhibition of glycolysis is not an option as clinical trials have shown ineffectiveness or unwanted side effects. We argue that systemic therapeutic inhibition of OXPHOS is not an option either because the anti-cancer effects of ROS production in healthy cells is inhibited as well. Therefore, we advocate to remove GSCs out of their hypoxic niches by the inhibition of their binding to niches to enable their differentiation and thus increase their sensitivity to radiotherapy and/or chemotherapy.
Keywords: glioblastoma stem cells, IDH1-mutation, energy metabolism
Published in DiRROS: 05.08.2024; Views: 358; Downloads: 270
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715. From plastics to microplastics and organismsOliver Bajt, 2021, review article Abstract: The amount of plastic waste and microplastics released into marine environments has increased rapidly in recent decades. The durability of plastic materials results in major problems following their release into the environment. This study provides an overview of recent findings on issues related to plastic degradation, the accumulation of microplastics in mussels and fishes, and the toxicological effects associated with the ingestion of microplastics. These findings confirm the serious problem of slowly degrading plastics (which rarely degrade fully) in natural marine environments. Microplastics have become widespread pollutants and have been detected in mussels and fish around the world. Microplastic particles, whether virgin or with adsorbed pollutants on their surfaces, pose a health problem after being ingested by marine organisms. This paper ends by highlighting the need for certain improvements in studies of these phenomena.
Published in DiRROS: 05.08.2024; Views: 303; Downloads: 178
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716. Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impactsAmalia Rosner, Jean Armengaud, Loriano Ballarin, Stéphanie Barnay-Verdier, Francesca Cima, Ana Varela Coelho, Isabelle Domart-Coulon, Damjana Drobne, Anne-Marie Geneviere, Anita Jemec Kokalj, Ewa Kotlarska, Andreja Ramšak, 2021, review article Abstract: Environmental stressors are assessed through methods that quantify their impacts on a wide range of metrics including species density, growth rates, reproduction, behaviour and physiology, as on host-pathogen interactions and immunocompetence. Environmental stress may induce additional sublethal effects, like mutations and epigenetic signatures affecting offspring via germline mediated transgenerational inheritance, shaping phenotypic plasticity, increasing disease susceptibility, tissue pathologies, changes in social behaviour and biological invasions.
The growing diversity of pollutants released into aquatic environments requires the development of a reliable, standardised and 3R (replacement, reduction and refinement of animals in research) compliant in vitro toolbox. The tools have to be in line with REACH regulation 1907/2006/EC, aiming to improve strategies for potential ecotoxicological risks assessment and monitoring of chemicals threatening human health and aquatic environments.
Aquatic invertebrates' adult stem cells (ASCs) are numerous and can be pluripotent, as illustrated by high regeneration ability documented in many of these taxa. This is of further importance as in many aquatic invertebrate taxa, ASCs are able to differentiate into germ cells. Here we propose that ASCs from key aquatic invertebrates may be harnessed for applicable and standardised new tests in ecotoxicology. As part of this approach, a battery of modern techniques and endpoints are proposed to be tested for their ability to correctly identify environmental stresses posed by emerging contaminants in aquatic environments.
Consequently, we briefly describe the current status of the available toxicity testing and biota-based monitoring strategies in aquatic environmental ecotoxicology and highlight some of the associated open issues such as replicability, consistency and reliability in the outcomes, for understanding and assessing the impacts of various chemicals on organisms and on the entire aquatic environment. Following this, we describe the benefits of aquatic invertebrate ASC-based tools for better addressing ecotoxicological questions, along with the current obstacles and possible overhaul approaches.
Published in DiRROS: 05.08.2024; Views: 307; Downloads: 302
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717. Angiogenesis in gynecological cancers and the options for anti-angiogenesis therapyBahar Yetkin-Arik, Arnoud W. Kastelein, Ingeborg Klaassen, Charlotte H. J. R. Jansen, Yani P. Latul, Miloš Vittori, Aydan Biri, Korhan Kahraman, Arjan W. Griffioen, Frederic Amant, Christianne A. R. Lok, Reinier O. Schlingemann, Cornelis J. F. van Noorden, 2021, review article Abstract: Angiogenesis is required in cancer, including gynecological cancers, for the growth of primary tumors and secondary metastases. Development of anti-angiogenesis therapy in gynecological cancers and improvement of its efficacy have been a major focus of fundamental and clinical research. However, survival benefits of current anti-angiogenic agents, such as bevacizumab, in patients with gynecological cancer, are modest. Therefore, a better understanding of angiogenesis and the tumor microenvironment in gynecological cancers is urgently needed to develop more effective anti-angiogenic therapies, either or not in combination with other therapeutic approaches. We describe the molecular aspects of (tumor) blood vessel formation and the tumor microenvironment and provide an extensive clinical overview of current anti-angiogenic therapies for gynecological cancers. We discuss the different phenotypes of angiogenic endothelial cells as potential therapeutic targets, strategies aimed at intervention in their metabolism, and approaches targeting their (inflammatory) tumor microenvironment.
Keywords: angiogenesis, anti-angiogenic therapy, endothelial cells, endothelial cell metabolism, gynecological cancer, non-tip cells, tip cells, tumor microenvironment, vascular disrupting agents
Published in DiRROS: 05.08.2024; Views: 257; Downloads: 208
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718. Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pestsSébastien Massart, Ian Adams, Maher Al Rwahnih, Steve Baeyen, Guillaume J. Bilodeau, Arnaud G. Blouin, Neil Boonham, Thierry Candresse, Anne Chandellier, Kris De Jonghe, Denis Kutnjak, Nataša Mehle, 2022, review article Abstract: High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health.
Published in DiRROS: 05.08.2024; Views: 293; Downloads: 272
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719. Organelles and phytohormones : a network of interactions in plant stress responsesAndras Bittner, Agata Cieśla, Kristina Gruden, Tjaša Lukan, Sakil Mahmud, Markus Teige, Ute Vothknecht, Bernhard Wurzinger, 2022, review article Abstract: Phytohormones are major signaling components that contribute to nearly all aspects of plant life. They constitute an interconnected communication network to fine-tune growth and development in response to the ever-changing environment. To this end, they have to coordinate with other signaling components, such as reactive oxygen species and calcium signals. On the one hand, the two endosymbiotic organelles, plastids and mitochondria, control various aspects of phytohormone signaling and harbor important steps of hormone precursor biosynthesis. On the other hand, phytohormones have feedback actions on organellar functions. In addition, organelles and phytohormones often act in parallel in a coordinated matter to regulate cellular functions. Therefore, linking organelle functions with increasing knowledge of phytohormone biosynthesis, perception, and signaling will reveal new aspects of plant stress tolerance. In this review, we highlight recent work on organelle–phytohormone interactions focusing on the major stress-related hormones abscisic acid, jasmonates, salicylic acid, and ethylene.
Keywords: abscisic acid (ABA), chloroplast, ethylene, mitochondria, jasmonates, plant organelles, phytohormones, salicylic acid (SA), plastids, stress signaling, retrograde signaling
Published in DiRROS: 05.08.2024; Views: 269; Downloads: 221
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720. TGA transcription factors : structural characteristics as basis for functional variabilityŠpela Tomaž, Kristina Gruden, Anna Coll Rius, 2022, review article Abstract: TGA transcription factors are essential regulators of various cellular processes, their activity connected to different hormonal pathways, interacting proteins and regulatory elements. Belonging to the basic region leucine zipper (bZIP) family, TGAs operate by binding to their target DNA sequence as dimers through a conserved bZIP domain. Despite sharing the core DNA-binding sequence, the TGA paralogues exert somewhat different DNA-binding preferences. Sequence variability of their N- and C-terminal protein parts indicates their importance in defining TGA functional specificity through interactions with diverse proteins, affecting their DNA-binding properties. In this review, we provide a short and concise summary on plant TGA transcription factors from a structural point of view, including the relation of their structural characteristics to their functional roles in transcription regulation.
Keywords: DOG1 domain, functional variability, intrinsically disordered regions, plant transcription regulation, post-translational modifications, structural characteristics, TGA transcription factors
Published in DiRROS: 05.08.2024; Views: 290; Downloads: 252
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