1111. 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, original scientific article Abstract: 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.
Keywords: cancer genomics, cBioPortal, data mining, epigenetics, gene expression, in silico
Published in DiRROS: 24.07.2024; Views: 368; Downloads: 551
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1112. 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, original scientific article Abstract: 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.
Keywords: pheromones, invasive organisms
Published in DiRROS: 24.07.2024; Views: 267; Downloads: 136
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1113. 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: 906; Downloads: 258
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1114. 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: 252; Downloads: 177
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1115. 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: 322; Downloads: 457
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1117. 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: 281; Downloads: 198
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1118. 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: 412; Downloads: 327
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1119. 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: 265; Downloads: 221
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1120. 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: 260; Downloads: 260
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