491. Lack of association between cortical amyloid deposition and glucose metabolism in early stage Alzheimer's disease patientsDaniela Ehrlich, Andreas Dunzinger, Gertraud Malsiner-Walli, Bettina Grün, Raffi Topakian, Marina Hodolič, Elmar Kainz, Robert Pichler, 2022, original scientific article Published in DiRROS: 24.07.2024; Views: 136; Downloads: 93
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492. Pre-treatment risk assessment of women with endometrial cancer: differences in outcomes of molecular and clinical classifications in the Slovenian patient cohortJure Knez, Monika Sobočan, Urška Belak Magdalenić, Rajko Kavalar, Mateja Zupin, Tomaž Büdefeld, Uroš Potočnik, Iztok Takač, 2022, original scientific article Published in DiRROS: 24.07.2024; Views: 167; Downloads: 139
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493. A model species for agricultural pest genomics : the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)Sean D. Schoville, Yolanda H. Chen, Martin N. Andersson, Joshua B. Benoit, Anita Bhandari, Julia H. Bowsher, Kristian Brevik, Kaat Cappelle, Mei-Ju M. Chen, Anna K. Childers, Kristina Gruden, Marko Petek, 2018, original scientific article Abstract: The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest. Keywords: colorado potato beetle, genome Published in DiRROS: 24.07.2024; Views: 165; Downloads: 131
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494. Decision support for the comparative evaluation and selection of analytical methods : detection of genetically modified organisms as an exampleDavid Dobnik, Kristina Gruden, Jana Žel, Yves Bertheau, Arne Holst-Jensen, Marko Bohanec, 2018, original scientific article Abstract: The selection of the best-fit-for-purpose analytical method to be implemented in the laboratory is difficult due to availability of multiple methods, targets, aims of detection, and different kinds and sources of more or less reliable information. Several factors, such as method performance, practicability, cost of setup, and running costs need to be considered together with personnel training when selecting the most appropriate method. The aim of our work was to prepare a flexible multicriteria decision analysis model suitable for evaluation and comparison of analytical methods used for the purpose of detecting and/or quantifying genetically modified organisms, and to use this model to evaluate a variety of changing analytical methods. Our study included selection of PCR-, isothermal-, protein-, microarray-, and next-generation sequencing-based methods in simplex and/or multiplex formats. We show that the overall result of their fitness for purpose is relatively similar; however, individual criteria or a group of related criteria exposed more substantial differences between the methods. The proposed model of this decision support system enables easy modifications and is thus suitable for any other application of complex analytical methods. Keywords: multicriteria decision analysis, genetically modified organisms, method evaluation, DEXi, decision support system, DSS Published in DiRROS: 24.07.2024; Views: 155; Downloads: 189
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495. Maristem - stem cells of marine/aquatic invertebrates : from basic research to innovative applicationsLoriano Ballarin, Baruch Rinkevich, Kestin Bartscherer, Artur Burzynski, Sebastien Cambier, Matteo Cammarata, Isabelle Domart-Coulon, Damjana Drobne, Juanma Encinas, Uri Frank, Anne-Marie Geneviere, Bert Hobmayer, Helike Löhelaid, Daniel Lyons, Pedro Martinez, Paola Oliveri, Lorena Perić, Stefano Piraino, Andreja Ramšak, Sebastian Rakers, Fabian Rentzsch, Amalia Rosner, Tiago Henriques da Silva, Ildiko Somorjai, Sherif Suleiman, Ana Varela Coelho, 2018, original scientific article Abstract: The “stem cells” discipline represents one of the most dynamic areas in biomedicine. While adult marine/aquatic invertebrate stem cell (MISC) biology is of prime research and medical interest, studies on stem cells from organisms outside the classical vertebrate (e.g., human, mouse, and zebrafish) and invertebrate (e.g., Drosophila, Caenorhabditis) models have not been pursued vigorously. Marine/aquatic invertebrates constitute the largest biodiversity and the widest phylogenetic radiation on Earth, from morphologically simple organisms (e.g., sponges, cnidarians), to the more complex mollusks, crustaceans, echinoderms, and protochordates. These organisms contain a kaleidoscope of MISC-types that allow the production of a large number of novel bioactive-molecules, many of which are of significant potential interest for human health. MISCs further participate in aging and regeneration phenomena, including whole-body regeneration. For years, the European MISC-community has been highly fragmented and has established scarce ties with biomedical industries in an attempt to harness MISCs for human welfare. Thus, it is important to (i) consolidate the European community of researchers working on MISCs; (ii) promote and coordinate European research on MISC biology; (iii) stimulate young researchers to embark on research in MISC-biology; (iv) develop, validate, and share novel MISC tools and methodologies; (v) establish the MISC discipline as a forefront interest of biomedical disciplines, including nanobiomedicine; and (vi) establish collaborations with industries to exploit MISCs as sources of bioactive molecules. In order to fill the recognized gaps, the EC-COST Action 16203 “MARISTEM” has recently been launched. At its initial stage, the consortium unites 26 scientists from EC countries, Cooperating countries, and Near Neighbor Countries. Keywords: aging, bioactive molecules, blue biotechnology, cancer, cell culture, COST Action, Europe, marine/aquatic invertebrates, regeneration, stem cells Published in DiRROS: 24.07.2024; Views: 360; Downloads: 113
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497. Surveillance of human enteric viruses in coastal waters using concentration with methacrylate monolithic supports prior to detection by RT-qPCRJosé Gonçalves, Ion Gutiérrez-Aguirre, Mukundh Narayanan Balasubramanian, Maja Zagorščak, Maja Ravnikar, Valentina Turk, 2018, original scientific article Abstract: This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior to molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at the Bay of Koper (Gulf of Trieste, Northern Adriatic Sea) and at a nearby bathing area and mussel farm areas.
RoV and NoV are released into the Bay of Koper, with higher rates close to the discharge of the wastewater treatment plant, however, they can be detected at recreational and mussel farming areas. Our results showed that water bodies considered safe based on FC concentrations, can still have low, yet potentially infective, concentrations of human viruses. Keywords: Rotavirus, Norovirus, faecal coliforms, RT-qPCR, methacrylate monolithic columns, enteric virus concentration Published in DiRROS: 24.07.2024; Views: 165; Downloads: 81
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498. NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate hostJean-Marie Volland, Arno Schintlmeister, Helena Zambalos, Siegfried Reipert, Patricija Mozetič, Salvador Espada-Hinojosa, Valentina Turk, Michael Wagner, Monika Bright, 2018, original scientific article Abstract: The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts. Keywords: microbial ecology, symbiosis Published in DiRROS: 24.07.2024; Views: 148; Downloads: 148
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499. Cell death is not sufficient for the restriction of potato virus Y spread in hypersensitive response-conferred resistance in potatoTjaša Lukan, Špela Baebler, Maruša Pompe Novak, Katja Guček, Maja Zagorščak, Anna Coll Rius, Kristina Gruden, 2018, original scientific article Abstract: Hypersensitive response (HR)-conferred resistance to viral infection restricts the virus spread and is accompanied by the induction of cell death, manifested as the formation of necrotic lesions. While it is known that salicylic acid is the key component in the orchestration of the events restricting viral spread in HR, the exact function of the cell death in resistance is still unknown. We show that potato virus Y (PVY) can be detected outside the cell death zone in Ny-1-mediated HR in potato plants (cv. Rywal), observed as individual infected cells or small clusters of infected cells outside the cell death zone. By exploiting the features of temperature dependent Ny-1-mediated resistance, we confirmed that the cells at the border of the cell death zone are alive and harbor viable PVY that is able to reinitiate infection. To get additional insights into this phenomenon we further studied the dynamics of both cell death zone expansion and occurrence of viral infected cell islands outside it. We compared the response of Rywal plants to their transgenic counterparts, impaired in SA accumulation (NahG-Rywal), where the lesions occur but the spread of the virus is not restricted. We show that the virus is detected outside the cell death zone in all lesion developmental stages of HR lesions. We also measured the dynamics of lesions expansion in both genotypes. We show that while rapid lesion expansion is observed in SA-depleted plants, virus spread is even faster. On the other hand the majority of analyzed lesions slowly expand also in HR-conferred resistance opening the possibility that the infected cells are eventually engulfed by cell death zone. Taken altogether, we suggest that the HR cell death is separated from the resistance mechanisms which lead to PVY restriction in Ny-1 genetic background. We propose that HR should be regarded as a process where the dynamics of events is crucial for effectiveness of viral arrest albeit the exact mechanism conferring this resistance remains unknown. Keywords: potato virus Y, salicylic acid, hypersensitive response, programmed cell death, callose deposits, necrotic lesion Published in DiRROS: 24.07.2024; Views: 149; Downloads: 138
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500. Plant X-tender : an extension of the AssemblX system for the assembly and expression of multigene constructs in plantsTjaša Lukan, Fabian Machens, Anna Coll Rius, Špela Baebler, Katrin Messerschmidt, Kristina Gruden, 2018, original scientific article Abstract: Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science. Keywords: cloning, plasmid construction, polymerase chain reaction Published in DiRROS: 24.07.2024; Views: 181; Downloads: 119
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