741. Poročilo o preskusu št.: LVG 2024-061 : vzorec št. 2024/00310Nikica Ogris, 2024, expertise, arbitration decision Keywords: varstvo gozdov, morfološke analize, črna jelša, Alnus glutinosa, list, rja, gliva, Melampsoridium betulinum Published in DiRROS: 17.07.2024; Views: 176; Downloads: 74
Full text (1,13 MB) |
742. Systematic comparison of nanopore and illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approachAnja Pecman, Ian Adams, Ion Gutiérrez-Aguirre, Adrian Fox, Neil Boonham, Maja Ravnikar, Denis Kutnjak, 2022, original scientific article Abstract: High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS. With this in mind, a study was completed, comparing the most established HTS platform (MiSeq benchtop sequencer—Illumina), with the MinION sequencer (Oxford Nanopore Technologies) for the detection of plant viruses and viroids. Method comparisons were performed on five selected samples, containing two viroids, which were sequenced using nanopore technology for the first time and 11 plant viruses with different genome organizations. For all samples, sequencing libraries for the MiSeq were prepared from ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) and for MinION sequencing, direct RNA sequencing of totRNA was used. Moreover, for one of the samples, which contained five different plant viruses and a viroid, three additional variations of sample preparation for MinION sequencing were also used: direct RNA sequencing of rRNA-depleted totRNA, cDNA-PCR sequencing of totRNA, and cDNA-PCR sequencing of rRNA-depleted totRNA. Whilst direct RNA sequencing of total RNA was the quickest of the tested approaches, it was also the least sensitive: using this approach, we failed to detect only one virus that was present in a sample at an extremely low titer. All other MinION sequencing approaches showed improved performance with outcomes similar to Illumina sequencing, with cDNA-PCR sequencing of rRNA-depleted totRNA showing the best performance amongst tested nanopore MinION sequencing approaches. Moreover, when enough sequencing data were generated, high-quality consensus viral genome sequences could be reconstructed from MinION sequencing data, with high identity to the ones generated from Illumina data. The results of this study implicate that, when an appropriate sample and library preparation are selected, nanopore MinION sequencing could be used for the detection of plant viruses and viroids with similar performance as Illumina sequencing. Taken as a balance of practicality and performance, this suggests that MinION sequencing may be an ideal tool for fast and affordable virus diagnostics. Keywords: high-throughput sequencing, plant virus, viroid detection, comparison, nanopore MinION sequencing, illumina MiSeq sequencing Published in DiRROS: 16.07.2024; Views: 181; Downloads: 144
Full text (2,84 MB) This document has many files! More... |
743. Diversity of dinoflagellate symbionts in scyphozoan hosts from shallow environments : the Mediterranean Sea and Cabo Frio (Rio de Janeiro, Brazil)Lucija Raspor Dall'Olio, Alfred Beran, Vesna Flander-Putrle, Alenka Malej, Andreja Ramšak, 2022, original scientific article Abstract: Symbiotic scyphozoan jellyfish are poorly understood in terms of their symbionts and traits, as well as the ecological significance of this association. Dinoflagellate symbionts of the medusae Cotylorhiza tuberculata, Phyllorhiza punctata, and Cassiopea xamachana collected in the Mediterranean Sea and Cabo Frio (Rio de Janeiro, Brazil) were phylogenetically identified based on 28S rDNA and ITS2 haplotypes. The studied medusae harbour only one phylotype of symbionts in a time, but scyphozoan jellyfishes can associate with several types of symbionts. This study confirmed that the main symbionts of investigated scyphozoans belong to the genera Symbiodinium, Philozoon, and Breviolum. The associations between dinoflagellate symbionts and Cotylorhiza tuberculata changed from year to year, hosting Philozoon one year and Breviolum another. Invasive species in the Mediterranean Sea Phyllorhiza punctata harboured dinoflagellate symbionts of genus Symbiodinium as in the native areal. Pigment analysis of two shallow-water symbiont species Breviolum sp. and Philozoon medusarum revealed characteristic profiles for each genus. Keywords: symbiodiniaceae, scyphozoa, 28S rDNA, ITS2, cultivation, pigments, marine biology Published in DiRROS: 16.07.2024; Views: 189; Downloads: 123
Full text (3,35 MB) This document has many files! More... |
744. Infiltrating natural killer cells bind, lyse and increase chemotherapy efficacy in glioblastoma stem-like tumorospheresBarbara Breznik, Meng-Wei Ko, Christopher Tse, Po-Chun Chen, Emanuela Senjor, Bernarda Majc, Anamarija Habič, Nicolas Angelillis, Metka Novak, Vera Župunski, Jernej Mlakar, David Nathanson, Anahid Jewett, 2022, original scientific article Abstract: Glioblastomas remain the most lethal primary brain tumors. Natural killer (NK) cell-based therapy is a promising immunotherapeutic strategy in the treatment of glioblastomas, since these cells can select and lyse therapy-resistant glioblastoma stem-like cells (GSLCs). Immunotherapy with super-charged NK cells has a potential as antitumor approach since we found their efficiency to kill patient-derived GSLCs in 2D and 3D models, potentially reversing the immunosuppression also seen in the patients. In addition to their potent cytotoxicity, NK cells secrete IFN-γ, upregulate GSLC surface expression of CD54 and MHC class I and increase sensitivity of GSLCs to chemotherapeutic drugs. Moreover, NK cell localization in peri-vascular regions in glioblastoma tissues and their close contact with GSLCs in tumorospheres suggests their ability to infiltrate glioblastoma tumors and target GSLCs. Due to GSLC heterogeneity and plasticity in regards to their stage of differentiation personalized immunotherapeutic strategies should be designed to effectively target glioblastomas. Keywords: glioblastoma, natural killer cells, translational oncology Published in DiRROS: 16.07.2024; Views: 202; Downloads: 180
Full text (10,81 MB) This document has many files! More... |
745. Fermentative indole production via bacterial tryptophan synthase alpha subunit and plant indole-3-glycerol phosphate lyase enzymesLenny Ferrer, Melanie Mindt, Maria Suarez-Diez, Tatjana Jilg, Maja Zagorščak, Jin-Ho Lee, Kristina Gruden, Volker F. Wendisch, Katarina Cankar, 2022, original scientific article Abstract: Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol phosphate (IGP) by plant indole-3-glycerol phosphate lyases (IGLs). While it is widely accepted that the tryptophan synthase α-subunit (TSA) has intrinsically low IGL activity in the absence of the tryptophan synthase β-subunit, in this study, we show that Corynebacterium glutamicum TSA functions as a bona fide IGL and can support fermentative indole production in strains providing IGP. By bioprospecting additional bacterial TSAs and plant IGLs that function as bona fide IGLs were identified. Capturing indole in an overlay enabled indole production to titers of about 0.7 g L–1 in fermentations using C. glutamicum strains expressing either the endogenous TSA gene or the IGL gene from wheat. Keywords: Corynebacterium glutamicum, indole, indole-3-glycerol phosphate lyase, tryptophan synthase α-subunit, bioprospecting, fermentative production Published in DiRROS: 16.07.2024; Views: 176; Downloads: 157
Full text (2,24 MB) This document has many files! More... |
746. New records of rare species in the Mediterranean Sea (May 2022)Vasiliki Kousteni, Athanasios Anastasiadis, Michel Bariche, Pietro Battaglia, Andrea Bonifazi, Ilija Ćetković, Giovanni Chimienti, Marco Colombo, Costas Constantinou, Maria Corsini-Foka, Cem Dalyan, Aikaterini Dogrammatzi, Filippo Domenichetti, Radhouan El Zrelli, Alfredo Fernández-Alías, Thodoros E. Kampouris, Lovrenc Lipej, Borut Mavrič, Ana Pešić, Domen Trkov, 2022, original scientific article Abstract: This Collective Article presents new information about the occurrence of 20 taxa that belong to six Phyla: one Cnidaria, one Ctenophora, two Annelida, four Mollusca, two Arthropoda, and ten Chordata. These records were reported from ten countries from the western to the eastern Mediterranean Sea as follows: Spain: early colonization signs of the Mar Menor lagoon by the cigar jellyfish Olindias muelleri; France: second record of the sea chub of the genus Kyphosus in French Mediterranean waters; Italy: first record of the marbled crab Pachygrapsus maurus in Sardinian waters; first records of the polychaetes Malmgrenia polypapillata and Levinsenia tribranchiata in the Tyrrhenian Sea; new record of the deep-sea squid Ancistrocheirus lesueurii in the Tyrrhenian Sea; first record of the pignosed arrowtooth eel Dysomma brevirostre in the Adriatic Sea; Tunisia: first documented record of the blue butterfish Stromateus fiatola and new record of the iconic great white shark Carcharodon carcharias in the Gulf of Gabes; Slovenia: first records of the sea slug Diaphorodoris alba and the sharpnose sevengill shark Heptranchias perlo; Mon-tenegro: new record of the rare tope shark Galeorhinus galeus; Greece: new records of the rabbitfish Chimaera monstrosa and the electric ray Tetronarce nobiliana; first published record of the nuribranch Discodoris rosi; Turkey: first record of the ctenophore Hormiphora plumosa at country level; first records of the anomuran decapod Munida speciosa and the Mediterranean tripodfish, Bathypterois mediterraneus from the Levantine Sea; Cyprus: first documented record of the nuribranch Scyllaea pelagica; Leb-anon: first record of the killer whale Orcinus orca from the Levantine Sea. Published in DiRROS: 16.07.2024; Views: 188; Downloads: 142
Full text (7,37 MB) This document has many files! More... |
747. Evaluating seagrass meadow dynamics by integrating field-based and remote sensing techniquesDanijel Ivajnšič, Martina Orlando-Bonaca, Daša Donša, Jaša Veno Grujić, Domen Trkov, Borut Mavrič, Lovrenc Lipej, 2022, original scientific article Abstract: Marine phanerogams are considered biological sentinels or indicators since any modification in seagrass meadow distribution and coverage signals negative changes in the marine environment. In recent decades, seagrass meadows have undergone global losses at accelerating rates, and almost one-third of their coverage has disappeared globally. This study focused on the dynamics of seagrass meadows in the northern Adriatic Sea, which is one of the most anthropogenically affected areas in the Mediterranean Sea. Seagrass distribution data and remote sensing products were utilized to identify the stable and dynamic parts of the seagrass ecosystem. Different seagrass species could not be distinguished with the Sentinel-2 (BOA) satellite image. However, results revealed a generally stable seagrass meadow (283.5 Ha) but, on the other hand, a stochastic behavior in seagrass meadow retraction (90.8 Ha) linked to local environmental processes associated with anthropogenic activities or climate change. If systemized, this proposed approach to monitoring seagrass meadow dynamics could be developed as a spatial decision support system for the entire Mediterranean basin. Such a tool could serve as a key element for decision makers in marine protected areas and would potentially support more effective conservation and management actions in these highly productive and important environments. Keywords: Adriatic Sea, seagrass meadow, change analysis, Cimodocea nodosa, image classifiers, Sentinel-2, marine biology, hydrobiology Published in DiRROS: 16.07.2024; Views: 155; Downloads: 144
Full text (3,45 MB) This document has many files! More... |
748. Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the oceanMario Pinto, Zihao Zhao, Katja Klun, Eugen Libowitzky, Gerhard J. Herndl, 2022, original scientific article Abstract: Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analyzed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for 2 years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harbored genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase, respectively. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This report identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential for utilizing LDPE-associated compounds as carbon and energy source.
IMPORTANCE Low-density polyethylene (LDPE) is one of the most used plastics worldwide, and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements, and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After 2 years of incubation, two of the microbial communities exhibited very similar taxonomic compositions mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean that might have the potential to degrade LDPE-associated compounds and that alkane degradation pathways might be involved. Keywords: LDPE, ocean, biodegradation, biofilms, metagenomics Published in DiRROS: 16.07.2024; Views: 261; Downloads: 126
Full text (6,01 MB) This document has many files! More... |
749. Inventory and DNA-barcode library of ground-dwelling predatory arthropods from Krokar virgin forest, SloveniaŽan Kuralt, Urška Ratajc, Neža Pajek Arambašić, Maja Ferle, Matic Gabor, Ivan Kos, 2022, original scientific article Abstract: Background
At a time of immense human pressure on nature and the resulting global environmental changes, the inventory of biota - especially of undisturbed natural areas - is of unprecedented value as it provides a baseline for future research. Krokar, an example of such an undisturbed area, is the largest virgin forest remnant in Slovenia. It is located in the Dinaric Alps, which are believed to harbour the most diverse fauna of soil invertebrates in Europe. Nevertheless, the soil fauna of the Krokar virgin forest has not been thoroughly studied. Moreover, modern taxonomic approaches often rely on genetic information (e.g. DNA-barcodes), while extensive reference libraries from the Dinaric area are lacking. Our work, therefore, focused on addressing this lack of faunistic and genetic data from the Dinaric area.
New information
A total of 2336 specimens belonging to 100 taxa (45 spiders, 30 centipedes, 25 ground-dwelling beetles) were collected and deposited to GBIF. DNA-barcodes of 124 specimens belonging to 73 species were successfully obtained and deposited in GenBank and BOLD databases. Keywords: zoology, faunistics, primary forest, Slovenia Published in DiRROS: 16.07.2024; Views: 172; Downloads: 73
Full text (458,32 KB) This document has many files! More... |
750. A new obligate groundwater species of Asellus (Isopoda, Asellidae) from IranMohammad Javad Malek-Hosseini, Jure Jugovic, Yaser Fatemi, Matjaž Kuntner, Rok Kostanjšek, Christophe J. Douady, Florian Malard, 2022, original scientific article Abstract: With only 43 described stygobionts and only two isopod species the obligate groundwater fauna of Iran, a vast country with over 10% of limestone surface, is inadequately known. Here, we report the discovery of Asellus ismailsezarii sp. nov. from Zagros mountains, the first eyeless and depigmented asellid isopod from Iran. The new species is morphologically similar to Asellus monticola Birstein, 1932, but it is eyeless and fully depigmented, has a slightly curved pereopod IV and does not bear any setae on proximal margins of exopodite of pleopods IV and V. Species phylogenetic relationships using original and datamined mitochondrial DNA and nuclear rDNA, and estimation of molecular divergences with other Asellus species, suggest that A. ismailsezarii sp. nov. is sister to a larger clade that also contains the European A. aquaticus species complex. Surface populations of Asellus have colonized groundwater at multiple occasions and localities, both in Europe and Asia, giving rise to species and subspecies that have evolved troglomorphisms, such as depigmentation and loss of eyes. Of the 37 formally described species and subspecies of Asellus, 15 are from groundwater, including A. ismailsezarii sp. nov. We predict that many more obligate groundwater Asellus taxa are yet to be discovered in Asia. Keywords: Asia, groundwater, molecular phylogeny, taxonomy, troglomorphy Published in DiRROS: 16.07.2024; Views: 183; Downloads: 145
Full text (4,11 MB) This document has many files! More... |