171. 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, original scientific article Abstract: 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.
Keywords: RNA silencing, plant defense response, Potato virus Y, molecular plant-virus interactions, microRNA, secondary small interfering RNA, small RNA sequencing, phasiRNA
Published in DiRROS: 24.07.2024; Views: 14; Downloads: 3
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172. Contrasting effects of altitude on species groups with different traits in a non-fragmented montane temperate forestMaarten De Groot, Al Vrezec, 2019, original scientific article Abstract: 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.
Keywords: climate change, Carabidae, Syrphidae, Aves, altitudinal gradient, species assemblage
Published in DiRROS: 24.07.2024; Views: 16; Downloads: 2
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173. Multiomics analysis of tolerant interaction of potato with potato virus YTjaša Stare, Živa Ramšak, Maja Križnik, Kristina Gruden, 2019, original scientific article Abstract: 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.
Keywords: potato cv. Désirée, potato virus Y
Published in DiRROS: 24.07.2024; Views: 5; Downloads: 3
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175. A taxonomic monograph of the liphistiid spider genus Heptathela, endemic to Japanese islandsXin Xu, Hirotsugu Ono, Matjaž Kuntner, Fengxiang Liu, Daiqin Li, 2019, original scientific article Abstract: Among the eight extant genera of primitively segmented spiders, family Liphistiidae, two are confined to East Asian islands, Heptathela Kishida, 1923 and Ryuthela Haupt, 1983. In this paper, a taxonomic revision of the genus Heptathela (Heptathelinae) from Kyushu and Ryukyu archipelago, Japan is provided. This study follows a multi-tier species delimitation strategy within an integrative taxonomic framework that is presented in a parallel paper, in which diagnosable lineages are considered as valid species. There, the initial hypothesis of species diversity (19) based on classical morphological diagnoses is tested with multiple species delimitation methods aimed at resolving conflict in data. This revision follows those analyses that converge on the species diversity of 20, which includes a pair of cryptic species that would have been undetected with morphology alone. After this revision, eight previously described species remain valid, two junior synonyms are proposed, and 12 new Heptathela species are described based on diagnostic evidence. To ease identification and to hint at putative evolutionary units, Heptathela is divided into three groups. The Kyushu group contains H. higoensis Haupt, 1983, H. kikuyai Ono, 1998, H. kimurai (Kishida, 1920), and H. yakushimaensis Ono, 1998; the Amami group contains H. amamiensis Haupt, 1983, H. kanenoi Ono, 1996, H. kojima sp. nov., H. sumiyo sp. nov., and H. uken sp. nov.; and the Okinawa group contains H. yanbaruensis Haupt, 1983, H. aha sp. nov., H. gayozan sp. nov., H. kubayama sp. nov., H. mae sp. nov., H. otoha sp. nov., H. shuri sp. nov., H. tokashiki sp. nov., H. unten sp. nov., and H. crypta sp. nov. Heptathela helios Tanikawa & Miyashita, 2014 is not assigned to a species group. A combination of diagnostic tools augments the morphological diagnoses that, in isolation, would be prone to error in morphologically challenging groups of organisms.
Keywords: Heptathelinae, island endemism, Kyushu, Ryukyu archipelago, species delimitation, trapdoor spiders
Published in DiRROS: 24.07.2024; Views: 3; Downloads: 1
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176. Linking farmer and beekeeper preferences with ecological knowledge to improve crop pollinationTom D. Breeze, Virginie Boreux, Lorna J. Cole, Lynn Dicks, Alexandra-Maria Klein, Gesine Pufal, Mario V. Balzan, Danilo Bevk, Laura Bortolotti, Theodora Petanidou, 2019, original scientific article Abstract: Pollination by insects is a key input into many crops, with managed honeybees often being hired to support pollination services. Despite substantial research into pollination management, no European studies have yet explored how and why farmers managed pollination services and few have explored why beekeepers use certain crops.
Using paired surveys of beekeepers and farmers in 10 European countries, this study examines beekeeper and farmer perceptions and motivations surrounding crop pollination.
Almost half of the farmers surveyed believed they had pollination service deficits in one or more of their crops.
Less than a third of farmers hired managed pollinators; however, most undertook at least one form of agri-environment management known to benefit pollinators, although few did so to promote pollinators.
Beekeepers were ambivalent towards many mass-flowering crops, with some beekeepers using crops for their honey that other beekeepers avoid because of perceived pesticide risks.
The findings highlight a number of largely overlooked knowledge gaps that will affect knowledge exchange and co-operation between the two groups.
Keywords: beekeeping, ecosystem services, pollination services, rural sociology
Published in DiRROS: 24.07.2024; Views: 17; Downloads: 3
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177. Influence of isothermal annealing in the 600 to 750 °C range on the degradation of SAF 2205 duplex stainless steelJaka Burja, Borut Žužek, Barbara Šetina, 2024, original scientific article Abstract: We studied the effect of isothermal annealing (600–750 °C, 1 to 1000 min) on the microstructure
and mechanical properties of SAF 2205 duplex stainless steel. Impact toughness was found
to be significantly more affected than hardness by annealing. Annealing at 750 °C for 1000 min
resulted in a more than 90% decrease in impact toughness, while hardness only increased by 25%.
Tensile strength increased up to 100 MPa, but elongation decreased by more than 50% under the
same conditions. Sigma phase formation was minimal at lower temperatures (650 °C and below)
but increased significantly at higher temperatures. At 750 °C and 1000 min of annealing, the ferrite
content dropped from 50% to 16%. These findings suggest that annealing temperature and time need
to be carefully controlled to avoid a reduction in impact toughness and ductility caused by sigma
phase precipitation. The harmful effect of sigma phase precipitation on mechanical properties was
directly shown.
Keywords: duplex stainless steel, sigma phase, precipitation kinetics, mechanical properties, isothermal annealing
Published in DiRROS: 24.07.2024; Views: 3; Downloads: 1
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178. Hyaluronic acid conjugates of glycine peptides and L-tryptophanFazilet Gürer, Tamilselvan Mohan, Matej Bračič, Ariana Barlič, Damjan Makuc, Janez Plavec, Karin Stana-Kleinschek, Rupert Kargl, 2024, original scientific article Published in DiRROS: 24.07.2024; Views: 8; Downloads: 4
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179. Tracking a mass mortality outbreak of pen shell Pinna nobilis populations : a collaborative effort of scientists and citizensMiguel Cabanellas-Reboredo, Maite Vázquez-Luis, Baptiste Mourre, Elvira Álvarez, Salud Deudero, Ángel Amores, Piero Addis, Enric Ballesteros, Agustín Barrajón, Stefania Coppa, Borut Mavrič, 2019, original scientific article Abstract: A mass mortality event is devastating the populations of the endemic bivalve Pinna nobilis in the Mediterranean Sea from early autumn 2016. A newly described Haplosporidian endoparasite (Haplosporidium pinnae) is the most probable cause of this ecological catastrophe placing one of the largest bivalves of the world on the brink of extinction. As a pivotal step towards Pinna nobilis conservation, this contribution combines scientists and citizens’ data to address the fast- and vast-dispersion and prevalence outbreaks of the pathogen. Therefore, the potential role of currents on parasite expansion was addressed by means of drift simulations of virtual particles in a high-resolution regional currents model. A generalized additive model was implemented to test if environmental factors could modulate the infection of Pinna nobilis populations. The results strongly suggest that the parasite has probably dispersed regionally by surface currents, and that the disease expression seems to be closely related to temperatures above 13.5 °C and to a salinity range between 36.5–39.7 psu. The most likely spread of the disease along the Mediterranean basin associated with scattered survival spots and very few survivors (potentially resistant individuals), point to a challenging scenario for conservation of the emblematic Pinna nobilis, which will require fast and strategic management measures and should make use of the essential role citizen science projects can play.
Keywords: mass mortality, endoparasites
Published in DiRROS: 24.07.2024; Views: 2; Downloads: 0
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180. Comparison of different methodologies and cryostat versus paraffin sections for chromogenic immunohistochemistryVashendriya V. V. Hira, Annique Loncq de Jong, Klea Ferro, Mohammed Khurshed, Remco J. Molenaar, Cornelis J. F. van Noorden, 2019, original scientific article Abstract: Immunohistochemistry (IHC) specifically localizes proteins in cells and tissues, but methodologies vary widely. Therefore, we performed a methodological IHC optimization and validation study. First, we compared advantages and disadvantages of cryostat sections versus paraffin sections. Second, we compared and optimized antigen retrieval in paraffin sections using citrate buffer and Tris/EDTA buffer. Third, aminoethyl carbazole (AEC) and 3,3'-diaminobenzidine (DAB) were tested as horseradish peroxidase (HRP) substrates to obtain a water-insoluble coloured end product to visualize antigens. Fourth, secondary antibodies conjugated with either mono-HRP or poly-HRP were compared. The study was performed using serial sections of human tonsil. IHC was performed with primary antibodies against endothelial cell marker CD31, smooth muscle actin (SMA), chemokine stromal-derived factor-1α (SDF-1α) and its receptor C-X-C receptor type 4 (CXCR4), macrophage marker CD68 and proliferation marker Ki67. DAB rather than AEC, and cryostat sections rather than paraffin sections gave optimum staining at highest primary antibody dilutions, whereas tissue morphology in paraffin sections was superior. Loss of antigenicity in paraffin sections by formaldehyde fixation, heat and/or masking of epitopes was counteracted by antigen retrieval but not for all antigens. Two out of six antigens (CD31 and CD68) could not be retrieved irrespective time and type of retrieval. Tris-EDTA was superior to citrate buffer for antigen retrieval. The use of mono-HRP or poly-HRP depended on the affinity of the primary antibody for its antigen. We conclude that IHC methodology optimization and validation are crucial steps for each antibody and each research question.
Keywords: immunohistochemistry, chromogens, aminoethyl carbazole, AEC, 3, 3'-diaminobenzidine, DAB, antigen retrieval, tonsil
Published in DiRROS: 24.07.2024; Views: 10; Downloads: 3
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