541. Rapid molecular detection and transmission of bacterial leaf streak pathogen, Xanthomonas oryzae pv. oryzicola, in rice seedsMark Paul Selda Rivarez, Elizabeth Parac, 2019, izvirni znanstveni članek Povzetek: Xanthomonas oryzae pv. oryzicola (Xoc) is a seed-borne bacterial pathogen of rice. In this study, a rapid molecular detection method in seeds was developed to prevent unwanted movement of infected materials and greater yield loss. Crude DNA from ground seed extract supernatant was precipitated in ethanol and centrifuged. DNA pellets of homogenous subsamples were pooled and werepurified using SDS or a DNA extraction kit. Three pairs of primers previously designed on Xoc isolate BLS-256 genome sequence robustly amplify Xoc-specific DNA sequences. Primer T40 was found to efficiently detect Xoc but only in single primer reactions. While primers 3864 and 3866 can amplify Xoc DNA separately, however, their multiplex PCR reactions were unsuccessful, probably due to substrate competition in the reaction mixture. Optimized PCR mixture and conditions were able to detect as low as 10 cfu/mL Xoc cells and the direct extraction method and conditions were able to detect as low as 104 cfu/mL inoculated cells using primer T40. Lastly, Xoc transmission through seeds was observed only in plant samples which were heavily infected. Recovery from infection, at around 25-50% was also observed in some cultivars which also manifested good grain filling at 56 days after transplanting. Objavljeno v DiRROS: 24.07.2024; Ogledov: 140; Prenosov: 93
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542. Golden orbweavers ignore biological rules : phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphismMatjaž Kuntner, Christopher A. Hamilton, Ren-Chung Cheng, Matjaž Gregorič, Nik Lupše, Tjaša Lokovšek, Emily Moriarty Lemmon, Alan R. Lemmon, Ingi Agnarsson, Jonathan A. Coddington, Jason E. Bond, 2019, izvirni znanstveni članek Povzetek: Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope’s rule (phyletic size increase), Rensch’s rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length
2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch’s rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope’s rule. Allometric analyses reject the converse, Rensch’s rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2–4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97–146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous GeratonephilaPoinar and Buckley (2012), Herennia Thorell 1877, IndoetraKuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and TrichonephilaDahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage. Ključne besede: spiders, evolution of sexual size dimorphism, golden orbweavers, analyses Objavljeno v DiRROS: 24.07.2024; Ogledov: 308; Prenosov: 161
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543. Expression patterns of endothelial permeability pathways in the development of the blood-retinal barrier in miceAnne-Eva van der Wijk, Joanna Wisniewska-Kruk, Ilse M.C. Vogels, Henk A. van Veen, Wing Fung Ip, Nicole N. van der Wel, Cornelis J. F. van Noorden, Reinier O. Schlingemann, Ingeborg Klaassen, 2019, izvirni znanstveni članek Povzetek: Insight into the molecular and cellular processes in blood-retinal barrier (BRB) development, including the contribution of paracellular and transcellular pathways, is still incomplete but may help to understand the inverse process of BRB loss in pathologic eye conditions. In this comprehensive observational study, we describe in detail the formation of the BRB at the molecular level in physiologic conditions, using mice from postnatal day (P)3 to P25. Our data indicate that immature blood vessels already have tight junctions at P5, before the formation of a functional BRB. Expression of the endothelial cell-specific protein plasmalemma vesicle-associated protein (PLVAP), which is known to be involved in transcellular transport and associated with BRB permeability, decreased during development and was absent when a functional barrier was formed. Moreover, we show that PLVAP deficiency causes a transient delay in retinal vascular development and changes in mRNA expression levels of endothelial permeability pathway proteins.—Van der Wijk, A.-E., Wisniewska-Kruk, J., Vogels, I. M. C., van Veen, H. A., Ip, W. F., van der Wei, N. N., van Noorden, C. J. F., Schlingemann, R. O., Klaassen, I. Expression patterns of endothelial permeability pathways in the development of the blood-retinal barrier in mice. Ključne besede: tight junctions, transcellular permeability, VEGF signaling Objavljeno v DiRROS: 24.07.2024; Ogledov: 174; Prenosov: 125
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544. Bioactive compounds in the oils of the autochthonous slovenian olive varieties ‘Buga’, ‘Črnica’ and ‘Drobnica’Vasilij Valenčič, Milena Bučar-Miklavčič, Maja Podgornik, 2024, izvirni znanstveni članek Povzetek: The adaptation of autochthonous olive varieties to local soil and climatic conditions can lead to a unique chemical composition and characteristics of olive oils that may differ from the generally accepted quality standards set out in the International Olive Oil Council strategy documents and EU regulations. Therefore, the fatty acid composition, biophenol, tocopherol, sterol and triterpenic dialcohol content and composition of the autochthonous Slovenian olive varieties ‘Buga’, ‘Crnica’ ˇ and ‘Drobnica’ were studied for a three-year period with the aim of valorising the characteristics of the three olive varieties. Standardised and accredited analytical methods in accordance with SIST EN ISO/IEC 17025:2017 were applied. The results of the investigation showed that the highest average amount of oleic acid (75.75%) was found in the oils of the ‘Crnica’ variety, followed by the ‘Drobnica’ ˇ (72.06%) and the ‘Buga’ (68.73%). All three varieties are a good source of total biophenols (‘Buga’ 616 mg/kg, ‘Drobnica’ 569 mg/kg and ‘Crnica’ 427 mg/kg) and ˇ α-tocopherol (‘Buga’ 378 mg/kg, ‘Drobnica’ 279 mg/kg, and ‘Crnica’ 243 mg/kg). ‘Buga’ and ‘Drobnica’ are characterised by high ˇ amounts of total sterols, 2468 mg/kg and 2391 mg/kg, respectively, while ‘Crnica’ oils, in comparison, ˇ showed a lower average value of total sterols (1351 mg/kg). Due to their exceptional chemical composition, ‘Buga’, ‘Crnica’ and ‘Drobnica’ show great potential for the further cultivation and ˇ valorisation of traditional olive oil production in the region, thus contributing to the preservation of biodiversity and local traditions. The quality parameters of olive oil from the autochthonous Slovenian olive varieties ‘Buga’, ‘Crnica’ and ‘Drobnica’ also fulfil the limits for extra virgin olive oil ˇ according to the Commission Delegated Regulation (EU) 2022/2104, despite local climatic influences. However, accelerated growth due to climatic changes affecting early harvest can lead to them falling outside these limits, which was observed in particular for the ‘Buga’ variety in terms of the linoleic acid content. This study emphasises the importance of timing the harvest to achieve optimum maturity and meet EU quality standards, taking into account the genetic makeup of the varieties and their response to the current climatic conditions. Ključne besede: olive, autochthonous Slovenian olive varieties, olive oil, bioactive compounds, chemistry, characterisation Objavljeno v DiRROS: 24.07.2024; Ogledov: 147; Prenosov: 73
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545. A simple in silico approach to generate gene-expression profiles from subsets of cancer genomics dataMohammed Khurshed, Remco J. Molenaar, Cornelis J. F. van Noorden, 2019, izvirni znanstveni članek Povzetek: In biomedical research, large-scale profiling of gene expression has become routine and offers a valuable means to evaluate changes in onset and progression of diseases, in particular cancer. An overwhelming amount of cancer genomics data has become publicly available, and the complexity of these data makes it a challenge to perform in silico data exploration, integration and analysis, in particular for scientists lacking a background in computational programming or informatics. Many web interface tools make these large datasets accessible but are limited to process large datasets. To accelerate the translation of genomic data into new insights, we provide a simple method to explore and select data from cancer genomic datasets to generate gene-expression profiles of subsets that are of specific genetic, biological or clinical interest. Ključne besede: cancer genomics, cBioPortal, data mining, epigenetics, gene expression, in silico Objavljeno v DiRROS: 24.07.2024; Ogledov: 259; Prenosov: 470
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546. A male-produced aggregation-sex pheromone of the beetle Arhopalus rusticus (Coleoptera: Cerambycidae, Spondylinae) may be useful in managing this invasive speciesAlenka Žunič Kosi, Nataša Stritih Peljhan, Yunfan Zou, J. Steven McElfresh, Jocelyn G. Millar, 2019, izvirni znanstveni članek Povzetek: The longhorned beetle Arhopalus rusticus (Coleoptera: Cerambycidae, Spondylinae) is a common species in conifer forests of the Northern Hemisphere, but with global trade, it has invaded and become established in New Zealand, Australia, and South America. Arhopalus rusticus is a suspected vector of the phytopathogenic nematode, Bursaphelenchus xylophilus, the causative agent of pine wilt disease, which is a major threat to pine forests worldwide. Here, we report the identification of a volatile, male-produced aggregation-sex pheromone for this species. Headspace odours from males contained a major male-specific compound, identified as (2 S, 5E)-6,10-dimethyl-5,9-undecadien-2-ol (common name (S)-fuscumol), and a minor component (E)-6,10-dimethyl-5,9-undecadien-2-one (geranylacetone). Both compounds are known pheromone components for species in the same subfamily. In field trials in its native range in Slovenia, (S)-fuscumol was significantly more attractive to beetles of both sexes, than racemic fuscumol and a blend of host plant volatiles commonly used as an attractant for this species. Fuscumol-baited traps also caught significant numbers of another spondylidine species, Spondylis buprestoides (L.), and a rare click beetle, Stenagostus rufus (De Geer). The pheromone can be exploited as a cost-effective and environmentally safe tool for detection and monitoring of this invasive species at ports of entry, and for monitoring the beetle’s distribution and population trends in both endemic and invasive populations. Ključne besede: pheromones, invasive organisms Objavljeno v DiRROS: 24.07.2024; Ogledov: 166; Prenosov: 101
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547. Potato virus Y infection alters small RNA metabolism and immune response in tomatoMaria I. Prigigallo, Maja Križnik, Domenico De Paola, Domenico Catalano, Kristina Gruden, Mariella M. Finetti-Sialer, Fabrizio Cillo, 2019, izvirni znanstveni članek Povzetek: Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype. Ključne besede: RNA silencing, plant defense response, Potato virus Y, molecular plant-virus interactions, microRNA, secondary small interfering RNA, small RNA sequencing, phasiRNA Objavljeno v DiRROS: 24.07.2024; Ogledov: 711; Prenosov: 154
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548. Contrasting effects of altitude on species groups with different traits in a non-fragmented montane temperate forestMaarten De Groot, Al Vrezec, 2019, izvirni znanstveni članek Povzetek: Temperature has strong effects on species composition and traits. These effects can differ within and between species groups. Thermoregulation and mobility are traits which can be strongly affected by altitudinal distribution. Our aim was to investigate the influence of altitude on the species richness, abundance and composition of species groups with different trophic, thermoregulatory and mobility traits. Carabids (Coleoptera; Carabidae), hoverflies (Diptera: Syrphidae) and birds (Aves: Passeriformes) were counted in three altitudinal belts with a total elevation difference of 700 m (from 300 m to 1000 m a.s.l.) in the same habitat type (non-fragmented temperate montane mixed beech and fir forest). We found that endotherms and more mobile species (i.e. birds) had a smaller turnover than ectotherms (i.e. hoverflies) and less mobile species (i.e. carabids), from which we can predict that the former species will undergo a less extreme shift than the latter in global warming scenarios. Species turnover across the altitudinal gradient increased from birds to hoverflies to carabid beetles. The effect of altitude on phenology was different between the studied ectotherm species groups (carabids and hoverflies). Hoverflies experience a phenological delay of species richness and abundance at higher altitudes in spring, but not at the end of summer, which implies that hoverfly phenology is affected by a change in temperature, while carabid beetle abundance exhibited a delay in phenology in summer at higher altitudes. We suggest that species that are expected to be most affected by climate change, such as ectotherms and species with poor dispersal ability should be prioritised as the best indicators for monitoring and conservation management purposes. Ključne besede: climate change, Carabidae, Syrphidae, Aves, altitudinal gradient, species assemblage Objavljeno v DiRROS: 24.07.2024; Ogledov: 142; Prenosov: 106
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549. Multiomics analysis of tolerant interaction of potato with potato virus YTjaša Stare, Živa Ramšak, Maja Križnik, Kristina Gruden, 2019, izvirni znanstveni članek Povzetek: Potato virus Y (PVY) is the most economically important viral pathogen of potato worldwide. Different potato cultivars react to the pathogen differently, resulting in resistant, tolerant or disease outcome of the interaction. Here we focus on tolerant interaction between potato cv. Désirée and PVYNTN. To capture the response in its full complexity, we analyzed the dynamic changes on multiple molecular levels, including transcriptomics, sRNAomics, degradomics, proteomics and hormonomics. The analysis was complemented by the measurements of viral accumulation, photosynthetic activity and phenotypisation of the symptoms. Besides cv. Désirée we also studied its transgenic counterpart depleted for the accumulation of salicylic acid (NahG-Désirée). This multiomics analysis provides better insights into the mechanisms leading to tolerant response of potato to viral infection and can be used as a base in further studies of plant immunity regulation. Ključne besede: potato cv. Désirée, potato virus Y Objavljeno v DiRROS: 24.07.2024; Ogledov: 174; Prenosov: 407
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