91. The digital MIQE guidelines update : minimum information for publication of quantitative digital PCR experiments for 2020Jim F. Huggett, Alexandra S. Whale, Ward De Spiegelaere, Afif M. Abdel Nour, Young-Kyung Bae, Vladimír Beneš, Dan Burke, Megan Cleveland, Philippe Corbisier, Alison S. Devonshire, Lianhua Dong, Daniela Drandi, Carole A. Foy, Jeremy A. Garson, Hua-Jun He, Jan Hellemans, Mikael Kubista, Antoon Lievens, Mike G. Makrigiorgos, Mojca Milavec, Reinhold D. Mueller, Tania Nolan, Denise M. O'Sullivan, Michael W. Pfaffl, Stefan Rödiger, Erica L. Romsos, Gregory L. Shipley, Valérie Taly, Andreas Untergasser, Carl T. Wittwer, Stephen A. Bustin, Jo Vandesompele, 2020, pregledni znanstveni članek Povzetek: Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology. Objavljeno v DiRROS: 06.08.2024; Ogledov: 140; Prenosov: 108
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92. Epithelial-to-mesenchymal transition as the driver of changing carcinoma and glioblastoma microenvironmentBernarda Majc, Tilen Sever, Miki Zarić, Barbara Breznik, Boris Turk, Tamara Lah Turnšek, 2020, pregledni znanstveni članek Povzetek: Epithelial-to-mesenchymal transition (EMT) is an essential molecular and cellular process that is part of normal embryogenesis and wound healing, and also has a ubiquitous role in various types of carcinoma and glioblastoma. EMT is activated and regulated by specific microenvironmental endogenous triggers and a complex network of signalling pathways. These mostly include epigenetic events that affect protein translation-controlling factors and proteases, altogether orchestrated by the switching on and off of oncogenes and tumour-suppressor genes in cancer cells. The hallmark of cancer-linked EMT is that the process is incomplete, as it is opposed by the reverse process of mesenchymal-to-epithelial transition, which results in a hybrid epithelial/mesenchymal phenotype that shows notable cell plasticity. This is a characteristic of cancer stem cells (CSCs), and it is of the utmost importance in their niche microenvironment, where it governs CSC migratory and invasive properties, thereby creating metastatic CSCs. These cells have high resistance to therapeutic treatments, in particular in glioblastoma. Ključne besede: carcinomas, cancer stem cellsInvasion, proteases, tumour microenvironment Objavljeno v DiRROS: 06.08.2024; Ogledov: 164; Prenosov: 162
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93. Between source and sea : the role of wastewater treatment in reducing marine microplasticsShirra Freeman, Andy M. Booth, Isam Sabbah, Rachel Tiller, Jan Dierking, Katja Klun, Ana Rotter, Eric Ben David, Jamileh Javidpour, Dror Angel, 2020, pregledni znanstveni članek Povzetek: Wastewater treatment plants (WWTPs) are a focal point for the removal of microplastic (MP) particles before they are discharged into aquatic environments. WWTPs are capable of removing substantial quantities of larger MP particles but are inefficient in removing particles with any one dimension of less than 100 μm, with influents and effluents tending to have similar quantities of these smaller particles. As a single WWTP may release >100 billion MP particles annually, collectively WWTPs are significant contributors to the problem of MP pollution of global surface waters. Currently, there are no policies or regulations requiring the removal of MPs during wastewater treatment, but as concern about MP pollution grows, the potential for wastewater technologies to capture particles before they reach surface waters has begun to attract attention. There are promising technologies in various stages of development that may improve the removal of MP particles from wastewater. Better incentivization could speed up the research, development and adoption of innovative practices. This paper describes the current state of knowledge regarding MPs, wastewater and relevant policies that could influence the development and deployment of new technologies within WWTPs. We review existing technologies for capturing very small MP particles and examine new developments that may have the potential to overcome the shortcomings of existing methods. The types of collaborations needed to encourage and incentivize innovation within the wastewater sector are also discussed, specifically strong partnerships among scientific and engineering researchers, industry stakeholders, and policy decision makers. Ključne besede: wastewater, microplastic, particle removal, innovation, policy, jellyfish mucus Objavljeno v DiRROS: 06.08.2024; Ogledov: 151; Prenosov: 65
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94. A perspective on the potential of using marine organic fertilizers for the sustainable management of coastal ecosystem servicesIraj Emadodin, Thorsten Reinsch, Ana Rotter, Martina Orlando-Bonaca, Friedhelm Taube, Jamileh Javidpour, 2020, pregledni znanstveni članek Povzetek: Agricultural production is predicted to double during the next century. To ensure food security in response to global population growth is a challenge and will require strategies that mitigate associated environmental damage in ways consistent with United Nation’s Sustainable Development Goals. One possible approach is to utilize organic fertilizers from marine sources to improve soil structure by enhancing activities of soil organisms and restoring essential plant nutrients to the soil. Here we identify opportunities to develop organic fertilizers from two types of materials of marine origin: seagrass wrack and jellyfish biomass. Seagrass wrack often occurs as undesirable waste material on beaches. In many coastal areas around the world jellyfish bloom presents a nuisance because of negative impacts on marine ecosystem productivity. Several investigations have reported that organic fertilizers produced from seagrass and jellyfish could enhance coastal ecosystem services by reducing pollution, and by improving soil health and quality. Recent research indicates that seagrass litter improves soil water holding capacity and the nutritional value of crops; moreover, it can be used as multi-functional fertilizer, due to its content of valuable macro- and microelements. The application of jellyfish fertilizer increases soil contents of organic matter, nitrogen, phosphorus and potassium and enhances the growth and survival of seedlings significantly. In this overview we describe novel approaches regarding the utilization of seagrass and jellyfish as sources of fertilizer, and experimental studies on the influences of marine organic fertilizers on soil restoration, and implications for coastal management. Ključne besede: seagrass, jellyfish, soil ecosystem, sustainable agriculture, soil fertility, blue economy Objavljeno v DiRROS: 06.08.2024; Ogledov: 161; Prenosov: 73
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95. Brain malignancies : glioblastoma and brain metastasesTamara Lah Turnšek, Metka Novak, Barbara Breznik, 2020, pregledni znanstveni članek Povzetek: Brain, the major organ of the central nervous system controls and processes most of body activities. Therefore, the most aggressive brain tumor – glioblastoma and metastases from other organs to the brain are lethal leaving the patients with very short time of survival. The brain tissue landscape is very different from any other tissues and the specific microenvironment, comprising stem cells niches and blood-brain barrier, significantly influences the low rate of glioblastoma metastasis out of the brain, but better accommodates brain-invading cancer. In contrast to low frequency (0.5%) of all glioblastoma metastases, 10%–45% of other primary cancers do metastasize to the brain. This review addresses general cellular and molecular pathways that are to some extent similar in both types of metastases, involving circulating tumor cells (CTCs) with cancer stem cells (CSCs) characteristics, and metastatic niches. The invasion is a dynamic process involving reversible epithelial-to-mesenchymal (EMT) cell process, creating a transient gradient state that is inter-connected with epigenetic plasticity of the metastasizing (m)CSCs. These cells can switch between stationary, low proliferating/dormant state to a migratory, mesenchymal-like state. Settling in their respective niches as dormant CSCs in the secondary organ is a common feature in all types of metastases. In glioblastoma metastasis, the malignant mGSC cells express markers of mesenchymal GSC subtype (MES-GSC), such as CD44 and YK-40 and their major obstacle seems to be propagating in the in various organs’ microenvironments, different from the niches that home GSCs in the primary glioblastoma. Focusing on one stromal component in the glioblastoma niches, the mesenchymal stem cells (MSCs), we report herein on their differential effects on glioblastoma cells, highly depending on their genetic subtype. On the other hand, in brain metastases, the major hindrance to metastatic progression of mCSCs seem to be crossing the blood-brain-barrier. Novel therapeutic approaches for brain metastases from various cancer types are advancing slowly, and the general trends involve targeting metastatic sub-clones and selective determinants of their niches. The update on the four most common brain metastases from lung, breast, melanoma and colorectal carcinoma is presented. Ključne besede: glioblastoma, cancer stem cells, invasion, metastasis, tumor microenvironment Objavljeno v DiRROS: 06.08.2024; Ogledov: 170; Prenosov: 113
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96. Stink bug communication and signal detection in a plant environmentAndrej Čokl, Alenka Žunič Kosi, Nataša Stritih Peljhan, Maria Carolina Blassioli Moraes, Raúl Alberto Laumann, Miguel Borges, 2021, pregledni znanstveni članek Povzetek: Plants influenced the evolution of plant-dwelling stink bugs’ systems underlying communication with chemical and substrate-borne vibratory signals. Plant volatiles provides cues that increase attractiveness or interfere with the probability of finding a mate in the field. Mechanical properties of herbaceous hosts and associated plants alter the frequency, amplitude, and temporal characteristics of stink bug species and sex-specific vibratory signals. The specificity of pheromone odor tuning has evolved through highly specific odorant receptors located within the receptor membrane. The narrow-band low-frequency characteristics of the signals produced by abdomen vibration and the frequency tuning of the highly sensitive subgenual organ vibration receptors match with filtering properties of the plants enabling optimized communication. A range of less sensitive mechanoreceptors, tuned to lower vibration frequencies, detect signals produced by other mechanisms used at less species-specific levels of communication in a plant environment. Whereas the encoding of frequency-intensity and temporal parameters of stink bug vibratory signals is relatively well investigated at low levels of processing in the ventral nerve cord, processing of this information and its integration with other modalities at higher neuronal levels still needs research attention. Objavljeno v DiRROS: 05.08.2024; Ogledov: 107; Prenosov: 113
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97. Extremophilic microorganisms in Central EuropeVera Zgonik, Janez Mulec, Tina Eleršek, Nives Ogrinc, Polona Jamnik, Nataša Poklar Ulrih, 2021, pregledni znanstveni članek Povzetek: Extremophiles inhabit a wide variety of environments. Here we focus on extremophiles in moderate climates in central Europe, and particularly in Slovenia. Although multiple types of stress often occur in the same habitat, extremophiles are generally combined into groups according to the main stressor to which they are adapted. Several types of extremophiles, e.g., oligotrophs, are well represented and diverse in subsurface environments and karst regions. Psychrophiles thrive in ice caves and depressions with eternal snow and ice, with several globally distributed snow algae and psychrophilic bacteria that have been discovered in alpine glaciers. However, this area requires further research. Halophiles thrive in salterns while thermophiles inhabit thermal springs, although there is little data on such microorganisms in central Europe, despite many taxa being found globally. This review also includes the potential use of extremophiles in biotechnology and bioremediation applications.
Ključne besede: ekstremofilni mikroorganizmi, mikrobna ekologija, ekstremofili, oligotrofi, psihrofili, halofili, termofili Objavljeno v DiRROS: 05.08.2024; Ogledov: 86; Prenosov: 109
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98. Valorization of marine waste : use of industrial by-products and beach wrack towards the production of high added-value productsVita Rudovica, Ana Rotter, Susana P. Gaudêncio, Lucie Novoveská, Füsun Akgül, Linn Kristin Akslen-Hoel, Diogo A. M. Alexandrino, Olga Anne, Lauris Arbidans, Miroslava Atanassova, Magdalena Bełdowska, Jacek Bełdowski, Amit Bhatnagar, Oskars Bikovens, Katja Klun, 2021, pregledni znanstveni članek Povzetek: Biomass is defined as organic matter from living organisms represented in all kingdoms. It is recognized to be an excellent source of proteins, polysaccharides and lipids and, as such, embodies a tailored feedstock for new products and processes to apply in green industries. The industrial processes focused on the valorization of terrestrial biomass are well established, but marine sources still represent an untapped resource. Oceans and seas occupy over 70% of the Earth’s surface and are used intensively in worldwide economies through the fishery industry, as logistical routes, for mining ores and exploitation of fossil fuels, among others. All these activities produce waste. The other source of unused biomass derives from the beach wrack or washed-ashore organic material, especially in highly eutrophicated marine ecosystems. The development of high-added-value products from these side streams has been given priority in recent years due to the detection of a broad range of biopolymers, multiple nutrients and functional compounds that could find applications for human consumption or use in livestock/pet food, pharmaceutical and other industries. This review comprises a broad thematic approach in marine waste valorization, addressing the main achievements in marine biotechnology for advancing the circular economy, ranging from bioremediation applications for pollution treatment to energy and valorization for biomedical applications. It also includes a broad overview of the valorization of side streams in three selected case study areas: Norway, Scotland, and the Baltic Sea. Objavljeno v DiRROS: 05.08.2024; Ogledov: 96; Prenosov: 92
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99. Global advances in tomato virome research : current status and the impact of high-throughput sequencingMark Paul Selda Rivarez, Ana Vučurović, Nataša Mehle, Maja Ravnikar, Denis Kutnjak, 2021, pregledni znanstveni članek Povzetek: Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato. Objavljeno v DiRROS: 05.08.2024; Ogledov: 101; Prenosov: 104
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100. The importance of jellyfish-microbe interactions for biogeochemical cycles in the oceanTinkara Tinta, Katja Klun, Gerhard J. Herndl, 2021, pregledni znanstveni članek Povzetek: 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. Objavljeno v DiRROS: 05.08.2024; Ogledov: 101; Prenosov: 89
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