11. Roles of the crotonyl-CoA carboxylase/reductase homologues in acetate assimilation and biosynthesis of immunosuppressant FK506 in Streptomyces tsukubaensisGregor Kosec, Hrvoje Petković, Špela Baebler, Kristina Gruden, Marko Blažič, 2015, original scientific article Abstract: Background
In microorganisms lacking a functional glyoxylate cycle, acetate can be assimilated by alternative pathways of carbon metabolism such as the ethylmalonyl-CoA (EMC) pathway. Among the enzymes converting CoA-esters of the EMC pathway, there is a unique carboxylase that reductively carboxylates crotonyl-CoA, crotonyl-CoA carboxylase/reductase (Ccr). In addition to the EMC pathway, gene homologues of ccr can be found in secondary metabolite gene clusters that are involved in the provision of structurally diverse extender units used in the biosynthesis of polyketide natural products. The roles of multiple ccr homologues in the same genome and their potential interactions in primary and secondary metabolic pathways are poorly understood.
Results
In the genome of S. tsukubaensis we have identified two ccr homologues; ccr1 is located in the putative ethylmalonyl-CoA (emc) operon and allR is located on the left fringe of the FK506 cluster. AllR provides an unusual extender unit allylmalonyl-CoA (ALL) for the biosynthesis of FK506 and potentially also ethylmalonyl-CoA for the related compound FK520. We have demonstrated that in S. tsukubaensis the ccr1 gene does not have a significant role in the biosynthesis of FK506 or FK520 when cultivated on carbohydrate-based media. However, when overexpressed under the control of a strong constitutive promoter, ccr1 can take part in the biosynthesis of ethylmalonyl-CoA and thereby FK520, but not FK506. In contrast, if ccr1 is inactivated, allR is not able to sustain a functional ethylmalonyl-CoA pathway (EMC) and cannot support growth on acetate as the sole carbon source, even when constitutively expressed in the chimeric emc operon. This is somewhat surprising considering that the same chimeric emc operon results in production of FK506 as well as FK520, consistent with the previously proposed relaxed specificity of AllR for C4 and C5 substrates.
Conclusions
Different regulation of the expression of both ccr genes, ccr1 and allR, and their corresponding pathways EMC and ALL, respectively, in combination with the different enzymatic properties of the Ccr1 and AllR enzymes, determine an almost exclusive role of ccr1 in the EMC pathway in S. tsukubaensis, and an exclusive role of allR in the biosynthesis of FK506/FK520, thus separating the functional roles of these two genes between the primary and secondary metabolic pathways.
Keywords: streptomicete, Streptomyces tsukubaensis, sekundarni metaboliti, takrolimus, FK506, biosinteze poliketidov
Published in DiRROS: 29.07.2024; Views: 16; Downloads: 6
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12. The effect of timing of female vibrational reply on male signalling and searching behaviour in the leafhopper Aphrodes makaroviMeta Virant-Doberlet, Maarten De Groot, Andrej Blejec, Ana Kuhelj, 2015, original scientific article Abstract: Sexual communication in animals often involves duetting characterized by a coordinated reciprocal exchange of acoustic signals. We used playback experiments to study the role of timing of a female reply in the species-specific duet structure in the leafhopper Aphrodes makarovi (Hemiptera: Cicadellidae). In leafhoppers, mate recognition and location is mediated exclusively by species- and sex-specific substrate-borne vibrational signals and a female signal emitted in reply to male advertisement calls is essential for recognition and successful location of the female. In A. makarovi, males have to initiate each exchange of vibrational signals between partners, and in a duet the beginning of a female reply overlaps the end of the male advertisement call. Results of playback treatments in which female replies were delayed and did not overlap with the male call revealed that in order to trigger an appropriate behavioural response of the male, female reply has to appear in a period less than 400 ms after the end of the initiating male call. Results also suggest that males are not able to detect a female reply while calling, since female reply that did not continue after the end of male call triggered male behaviour similar to behaviour observed in the absence of female reply. Together, our results show that vibrational duets are tightly coordinated and that the species-specific duet structure plays an important role in mate recognition in location processes.
Keywords: vibration, insects, bioacoustics, animal signaling and communication
Published in DiRROS: 29.07.2024; Views: 20; Downloads: 7
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13. PESI - a taxonomic backbone for EuropeYde De Jong, Davorin Tome, 2015, original scientific article Abstract: Background
Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.
The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.
New information
This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
Published in DiRROS: 29.07.2024; Views: 23; Downloads: 7
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14. Bimodal dynamics of primary metabolism-related responses in tolerant potato-Potato virus Y interactionNeža Turnšek, Živa Ramšak, Katja Stare, Tjaša Stare, Dominik Vodnik, Andrej Blejec, Kristina Gruden, Wolfram Weckwerth, Stefanie Wienkoop, 2015, original scientific article Abstract: Background
Potato virus Y (PVY) is a major pathogen that causes substantial economic losses in worldwide potato production. Different potato cultivars differ in resistance to PVY, from severe susceptibility, through tolerance, to complete resistance. The aim of this study was to better define the mechanisms underlying tolerant responses of potato to infection by the particularly aggressive PVYNTN strain. We focused on the dynamics of the primary metabolism-related processes during PVYNTN infection.
Results
A comprehensive analysis of the dynamic changes in primary metabolism was performed, which included whole transcriptome analysis, nontargeted proteomics, and photosynthetic activity measurements in potato cv. Désirée and its transgenic counterpart depleted for accumulation of salicylic acid (NahG-Désirée). Faster multiplication of virus occurred in the NahG-Désirée, with these plants developing strong disease symptoms. We show that while the dynamics of responses at the transcriptional level are extensive and bimodal, this is only partially translated to the protein level, and to the final functional outcome. Photosynthesis-related genes are transiently induced before viral multiplication is detected and it is down-regulated later on. This is reflected as a deficiency of the photosynthetic apparatus at the onset of viral multiplication only. Interestingly, specific and constant up-regulation of some RuBisCO transcripts was detected in Désirée plants, which might be important, as these proteins have been shown to interact with viral proteins.
In SA-deficient and more sensitive NahG-Désirée plants, consistent down-regulation of photosynthesis-related genes was detected. A constant reduction in the photochemical efficiency from the onset of viral multiplication was identified; in nontransgenic plants this decrease was only transient. The transient reduction in net photosynthetic rate occurred in both genotypes with the same timing, and coincided with changes in stomatal conductivity.
Conclusions
Down-regulation of photosynthesis-related gene expression and decreased photosynthetic activity is in line with other studies that have reported the effects of biotic stress on photosynthesis. Here, we additionally detected induction of light-reaction components in the early stages of PVYNTN infection of tolerant interaction. As some of these components have already been shown to interact with viral proteins, their overproduction might contribute to the absence of symptoms in cv. Désirée.
Keywords: plant-pathogen interactions, Potato virus Y, potyviridae, salicylic acid, whole transcriptome analysis, shot-gun proteomics, photosynthetic parameters
Published in DiRROS: 29.07.2024; Views: 14; Downloads: 7
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15. oVERFLOw project : Vulnerability assessment of embankments and bridges exposed to flooding hazards : Deliverable 6.4Valentina Bau', Mirko Kosič, Andrej Anžlin, Mario Bacic, 2022, final research report Abstract: This deliverable is a report on the development of a strategy for adaptation measures to flood events for the embankments, riverbanks and bridges, which can afterwards be used for the case study areas considered in the Overflow project. The deliverable presents a comprehensive approach that enables the choice of the best adaptation measures to overcome the vulnerability of critical infrastructure to flooding events. The most suitable countermeasures can therefore be selected based on the outcomes of the vulnerability assessment and risk forecasting tool. Such a strategy will be essential for the relevant authorities and IMs. The strategy proposes optimal adaptation measures depending on areas specificities, incorporating socio-economic and environmental multi-objective optimization.
Keywords: adaptation measures, countermeasures, vulnerability, flooding, resilience, embankments, bridges
Published in DiRROS: 29.07.2024; Views: 31; Downloads: 12
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16. Characterization of bloom iron smelting site remains in Pržanj, SloveniaJaka Burja, Barbara Šetina, Daša Pavlovič, 2024, original scientific article Abstract: This paper gives an overview of findings, connected with metallurgical activity, at the Pržanj archeological site near Ljubljana, Slovenia. More than 230 kg of slag and other remains connected with early medieval (from the 5th to the 12th century AD) metallurgical activities was found at the excavation site. The remains were grouped into four categories, i.e., furnace remains, ore, slag and a ferrous product, and analyzed in detail to obtain their chemical composition, microstructural characteristics, and mineral phase composition. The furnace wall remains, identified by their morphology and chemical composition, revealed an intensive iron processing activity at the site. The iron ore at the site was identified as goethite (FeO(OH)), a surprising find in Slovenia where limonite is typically used, and its presence suggests the potential exploitation of local bog iron ore, given the site’s geological context. Abundant slag remains at the site, identified by their shape, molten microstructure, and mineral components like wuestite, fayalite, and hercynite, indicated sophisticated smelting practices, including the use of CaO-rich materials to lower the melting temperature, a technique likely preserved from antiquity. Findings of ferrous products at ancient metallurgical sites are rare due to their value, but the discovery of a corroded iron bloom conglomerate at this site, initially mistaken for furnace remains, highlights the challenges in identifying small, corroded ferrous fragments that are often misidentified as ore. The results indicate extensive metallurgical activity at the excavation site, marking it as the first documented early medieval iron smelting production site in Slovenia.
Keywords: bloom iron, bloomery slag, archaeometallurgy, microstructure
Published in DiRROS: 29.07.2024; Views: 27; Downloads: 12
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17. Kakšen vpliv bo imela Evropska unija na izvedbo del v gozdovih?Amina Gačo, Matjaž Dovečar, Darja Stare, 2024, professional article Keywords: gozdarstvo, pridobivanje lesa, gozdarska dela, evropska zakonodaja, zakonodaja, Evropa
Published in DiRROS: 27.07.2024; Views: 87; Downloads: 13
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18. Pregled okoljskih, ekonomskih in socialnih meril za obravnavane tehnološke postopke pridobivanja lesaMartin Jež, Janez Krč, Matevž Triplat, 2024, professional article Keywords: gozdarstvo, pridobivanje lesa, okoljska merila, ekonomska merila, socialna merila
Published in DiRROS: 27.07.2024; Views: 78; Downloads: 18
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