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1.
A new tool for faster construction of marine biotechnology collaborative networks
Ana Rotter, Susana P. Gaudêncio, Katja Klun, Jan-Niklas Macher, Olivier Thomas, Irem Deniz, Christine Edwards, Ernesta Grigalionyte-Bembič, Z. Ljubešić, Johan Robbens, Giovanna Cristina Varese, Marlen I. Vasquez, 2021, drugi znanstveni članki

Povzetek: The increasing and rapid development in technologies, infrastructures, computational power, data availability and information flow has enabled rapid scientific advances. These entail transdisciplinary collaborations that maximize sharing of data and knowledge and, consequently, results, and possible technology transfer. However, in emerging scientific fields it is sometimes difficult to provide all necessary expertise within existing collaborative circles. This is especially true for marine biotechnology that directly addresses global societal challenges. This article describes the creation of a platform dedicated to facilitating the formation of short or mid-term collaborative networks in marine biotechnology. This online platform (https://www.ocean4biotech.eu/map/) enables experts (researchers and members of the marine biotechnology community in general) to have the possibility to showcase their expertise with the aim of being integrated into new collaborations/consortia on the one hand, or to use it as a search tool to complement the expertise in planned/running collaborations, on the other. The platform was created within the Ocean4Biotech (European transdisciplinary networking platform for marine biotechnology) Action, funded under the framework of the European Cooperation in Science and Technology (COST). To build the platform, an inquiry was developed to identify experts in marine biotechnology and its adjunct fields, to define their expertise, to highlight their infrastructures and facilities and to pinpoint the main bottlenecks in this field. The inquiry was open to all experts in the broad field of marine biotechnology, including non-members of the consortium. The inquiry (https://ee.kobotoolbox.org/single/UKVsBNtD) remains open for insertion of additional expertise and the resulting interactive map can be used as a display and search tool for establishing new collaborations.
Objavljeno v DiRROS: 06.08.2024; Ogledov: 43; Prenosov: 21
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2.
Editorial : marine biotechnology, revealing an ocean of opportunities
Ana Rotter, Susana P. Gaudêncio, Arita Dubnika, Marlen I. Vasquez, 2022, drugi znanstveni članki

Povzetek: The ocean, including its coastal areas and covering more than 70% of the Earth’s surface, has always represented an important environmental and economic resource. Indeed, almost 40% of the global population lives in coastal communities (United Nations, 2017). With its ecosystem services, the ocean represents a pivotal role in human society (Rayner et al., 2019). Undeniably, the ocean provides food, regulates the climate, provides oxygen and ensures economic resources through its shipping routes and tourism opportunities. Additionally, the ocean is home to organisms that have for centuries sparked the scientific interest of many research groups to uncover the biodiversity and functions of these fascinating marine ecosystems. Through their biological and chemical diversity, marine organisms synthesize unique secondary metabolites, biopolymers and enzymes produced in response to environmental stimuli. Secondary metabolites play important biological roles in improving competitiveness, providing chemical defence against predators or competitors and facilitating reproductive processes (Rotter et al.). Screening of these natural products and their producer organisms, coupled with the search of their unique biological activities that could be used in various industries, is tackled within marine (blue) biotechnology. Marine organisms and microorganisms can be investigated, and their primary and secondary metabolites, biopolymers and enzymes can be used as lead agents for nutraceutical and pharmaceutical industries to improve processes (e.g., in drug delivery) and as a source of bio-inspired materials for numerous biotechnological applications. Although this field has been appearing since the 1960s and 1970s, it is still considered an emerging field and marine biotechnology is still in its infancy (Rayner et al., 2019; Rotter et al.). This is because many marine environments are extreme ones that are either hardly accessible for sampling and harvesting and/or are home to organisms that cannot be cultured or grown in laboratory conditions. Consequently, a lot of advancement in the field of marine biotechnology was hampered until recent advances in science were achieved, including sampling methods, high-throughput methods and transdisciplinary collaborations.
Ključne besede: blue biotechnology, marine biotechnology, ocean bioprospecting, marine organisms
Objavljeno v DiRROS: 06.08.2024; Ogledov: 32; Prenosov: 18
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3.
Marine environmental plastic pollution : mitigation by microorganism degradation and recycling valorization
Juliana Oliveira, Afonso Belchior, Verônica D. Da Silva, Ana Rotter, Željko Petrovski, Pedro Lúcio Almeida, Nídia D. Lourenço, Susana P. Gaudêncio, 2020, pregledni znanstveni članek

Povzetek: Plastics are very useful materials and present numerous advantages in the daily life of individuals and society. However, plastics are accumulating in the environment and due to their low biodegradability rate, this problem will persist for centuries. Until recently, oceans were treated as places to dispose of litter, thus the persistent substances are causing serious pollution issues. Plastic and microplastic waste has a negative environmental, social, and economic impact, e.g., causing injury/death to marine organisms and entering the food chain, which leads to health problems. The development of solutions and methods to mitigate marine (micro)plastic pollution is in high demand. There is a knowledge gap in this field, reason why research on this thematic is increasing. Recent studies reported the biodegradation of some types of polymers using different bacteria, biofilm forming bacteria, bacterial consortia, and fungi. Biodegradation is influenced by several factors, from the type of microorganism to the type of polymers, their physicochemical properties, and the environment conditions (e.g., temperature, pH, UV radiation). Currently, green environmentally friendly alternatives to plastic made from renewable feedstocks are starting to enter the market. This review covers the period from 1964 to April 2020 and comprehensively gathers investigation on marine plastic and microplastic pollution, negative consequences of plastic use, and bioplastic production. It lists the most useful methods for plastic degradation and recycling valorization, including degradation mediated by microorganisms (biodegradation) and the methods used to detect and analyze the biodegradation.
Objavljeno v DiRROS: 06.08.2024; Ogledov: 36; Prenosov: 50
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4.
Between source and sea : the role of wastewater treatment in reducing marine microplastics
Shirra 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: 35; Prenosov: 30
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5.
A perspective on the potential of using marine organic fertilizers for the sustainable management of coastal ecosystem services
Iraj 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: 42; Prenosov: 32
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6.
Valorization of marine waste : use of industrial by-products and beach wrack towards the production of high added-value products
Vita 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: 51; Prenosov: 54
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7.
From the sea to aquafeed : a perspective overview
Orhan Tufan Eroldogan, Brett Glencross, Lucie Novoveská, Susana P. Gaudêncio, Buki Rinkevich, Giovanna Cristina Varese, Maria F. Carvalho, Deniz Tasdemir, Ivo Safarik, Soren Laurentius Nielsen, Céline Rebours, Lada Lukić-Bilela, Johan Robbens, Evita Strode, Berat Z. Haznedaroglu, Marlen I. Vasquez, Ivana Čabarkapa, Slađana Rakita, Katja Klun, Ana Rotter, 2023, pregledni znanstveni članek

Povzetek: Aquaculture has been one of the fastest-growing food production systems sectors for over three decades. With its growth, the demand for alternative, cheaper and high-quality feed ingredients is also increasing. Innovation investments on providing new functional feed alternatives have yielded several viable alternative raw materials. Considering all the current feed ingredients, their circular adaption in the aquafeed manufacturing industry is clearly of the utmost importance to achieve sustainable aquaculture in the near future. The use of terrestrial plant materials and animal by-products predominantly used in aquafeed ingredients puts a heavily reliance on terrestrial agroecosystems, which also has its own sustainability concerns. Therefore, the aquafeed industry needs to progress with functional and sustainable alternative raw materials for feed that must be more resilient and consistent, considering a circular perspective. In this review, we assess the current trends in using various marine organisms, ranging from microorganisms (including fungi, thraustochytrids, microalgae and bacteria) to macroalgae and macroinvertebrates as viable biological feed resources. This review focuses on the trend of circular use of resources and the development of new value chains. In this, we present a perspective of promoting novel circular economy value chains that promote the re-use of biological resources as valuable feed ingredients. Thus, we highlight some potentially important marine-derived resources that deserve further investigations for improving or addressing circular aquaculture.
Objavljeno v DiRROS: 05.08.2024; Ogledov: 42; Prenosov: 71
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8.
Insertion of a specific fungal 3'-phosphoadenosine-5'-phosphatase motif into a plant homologue improves halotoleranceand drought tolerance of plants
Meti Buh Gašparič, Metka Lenassi, Cene Gostinčar, Ana Rotter, Ana Plemenitaš, Nina Gunde-Cimerman, Kristina Gruden, Jana Žel, 2013, izvirni znanstveni članek

Povzetek: Soil salinity and drought are among the most serious agricultural and environmental problems of today. Therefore, investigations of plant resistance to abiotic stress have received a lot of attention in recent years. In this study, we identified the complete coding sequence of a 3′-phosphoadenosine-5′-phosphatase protein, ApHal2, from the halotolerant yeast Aureobasidium pullulans. Expression of the ApHAL2 gene in a Saccharomyces cerevisiae hal2 mutant complemented the mutant auxotrophy for methionine, and rescued the growth of the hal2 mutant in media with high NaCl concentrations. A 21-amino-acids-long region of the ApHal2 enzyme was inserted into the Arabidopsis thaliana homologue of Hal2, the SAL1 phosphatase. The inserted sequence included the META motif, which has previously been implicated in increased sodium tolerance of the Hal2 homologue from a related fungal species. Transgenic Arabidopsis plants overexpressing this modified SAL1 (mSAL1) showed improved halotolerance and drought tolerance. In a medium with an elevated salt concentration, mSAL1-expressing plants were twice as likely to have roots in a higher length category in comparison with the wild-type Arabidopsis and with plants overexpressing the native SAL1, and had 5% to 10% larger leaf surface area under moderate and severe salt stress, respectively. Similarly, after moderate drought exposure, the mSAL1-expressing plants showed 14% increased dry weight after revitalisation, with no increase in dry weight of the wild-type plants. With severe drought, plants overexpressing native SAL1 had the worst rehydration success, consistent with the recently proposed role of SAL1 in severe drought. This was not observed for plants expressing mSAL1. Therefore, the presence of this fungal META motif sequence is beneficial under conditions of increased salinity and moderate drought, and shows no drawbacks for plant survival under severe drought. This demonstrates that adaptations of extremotolerant fungi should be considered as a valuable resource for improving stress-tolerance in plant breeding in the future.
Ključne besede: soil salinity and drought, plant resistance, abiotic stress
Objavljeno v DiRROS: 02.08.2024; Ogledov: 119; Prenosov: 106
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9.
Expression analysis of all protease genes reveals cathepsin K to be overexpressed in glioblastoma
Urška Verbovšek, Helena Motaln, Ana Rotter, Nadia A. Atai, Kristina Gruden, Cornelis J. F. van Noorden, Tamara Lah Turnšek, 2014, izvirni znanstveni članek

Povzetek: Background Cancer genome and transcriptome analyses advanced our understanding of cancer biology. We performed transcriptome analysis of all known genes of peptidases also called proteases and their endogenous inhibitors in glioblastoma multiforme (GBM), which is one of the most aggressive and deadly types of brain cancers, where unbalanced proteolysis is associated with tumor progression. Methods Comparisons were performed between the transcriptomics of primary GBM tumors and unmatched non-malignant brain tissue, and between GBM cell lines (U87-MG and U373) and a control human astrocyte cell line (NHA). Publicly-available data sets and our own datasets were integrated and normalized using bioinformatics tools to reveal protease and protease inhibitor genes with deregulated expression in both malignant versus non-malignant tissues and cells. Results Of the 311 protease genes identified to be differentially expressed in both GBM tissues and cells, 5 genes were highly overexpressed, 2 genes coding for non-peptidase homologues transferrin receptor (TFRC) and G protein-coupled receptor 56 (GPR56), as well as 3 genes coding for the proteases endoplasmic reticulum aminopeptidase 2 (ERAP2), glutamine-fructose-6-phosphate transaminase 2 (GFPT2) and cathepsin K (CTSK), whereas one gene, that of the serine protease carboxypeptidase E (CPE) was strongly reduced in expression. Seventy five protease inhibitor genes were differentially expressed, of which 3 genes were highly overexpressed, the genes coding for stefin B (CSTB), peptidase inhibitor 3 (PI3 also named elafin) and CD74. Seven out of 8 genes (except CSTB) were validated using RT-qPCR in GBM cell lines. CTSK overexpression was validated using RT-qPCR in GBM tissues as well. Cathepsin K immunohistochemical staining and western blotting showed that only proteolytically inactive proforms of cathepsin K were overexpressed in GBM tissues and cells. Conclusions The presence of high levels of inactive proforms of cathepsin K in GBM tissues and cells indicate that in GBM the proteolytic/collagenolytic role is not its primary function but it plays rather a different yet unknown role.
Ključne besede: glioblastoma multiforme, genes
Objavljeno v DiRROS: 02.08.2024; Ogledov: 99; Prenosov: 120
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10.
Potato Virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack
Marko Petek, Ana Rotter, Polona Kogovšek, Špela Baebler, Axel Mithöfer, Kristina Gruden, 2014, izvirni znanstveni članek

Povzetek: In the field, plants are challenged by more than one biotic stressor at the same time. In this study, the molecular interactions between potato (Solanum tuberosum L.), Colorado potato beetle (Leptinotarsa decemlineata Say; CPB) and Potato virus YNTN (PVYNTN) were investigated through analyses of gene expression in the potato leaves and the gut of the CPB larvae, and of the release of potato volatile compounds. CPB larval growth was enhanced when reared on secondary PVYNTN-infected plants, which was linked to decreased accumulation of transcripts associated with the antinutritional properties of potato. In PVYNTN-infected plants, ethylene signalling pathway induction and induction of auxin response transcription factors were attenuated, while no differences were observed in jasmonic acid (JA) signalling pathway. Similarly to rearing on virus-infected plants, CPB larvae gained more weight when reared on plants silenced in JA receptor gene (coi1). Although herbivore-induced defence mechanism is regulated predominantly by JA, response in coi1-silenced plants only partially corresponded to the one observed in PVYNTN-infected plants, confirming the role of other plant hormones in modulating this response. The release of β-barbatene and benzyl alcohol was different in healthy and PVYNTN-infected plants before CPB larvae infestation, implicating the importance of PVYNTN infection in plant communication with its environment. This was reflected in gene expression profiles of neighbouring plants showing different degree of defence response. This study thus contributes to our understanding of plant responses in agro-ecosystems.
Ključne besede: insect midgut transcriptional response, gene expression, plant defence, volatile organic compounds, potato
Objavljeno v DiRROS: 02.08.2024; Ogledov: 84; Prenosov: 58
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