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2. MapMan4 : a refined protein classification and annotation framework applicable to multi-omics data analysisRainer Schwacke, Gabriel Y. Ponce-Soto, Kirsten Krause, Anthony M. Bolger, Borjana Arsova, Asis Hallab, Kristina Gruden, Mark Stitt, Marie E. Bolger, Björn Usadel, 2019, original scientific article Abstract: Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
Keywords: genome sequences, MapMan4
Published in DiRROS: 23.07.2024; Views: 1; Downloads: 0
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3. Microscopy of crustacean cuticle : formation of a flexible extracellular matrix in moulting sea slaters Ligia pallasiiJasna Štrus, Magda Tušek-Žnidarič, Urška Repnik, Andrej Blejec, Adam P. Summers, 2019, original scientific article Abstract: Structural and functional properties of exoskeleton in moulting sea slaters Ligia pallasii from the Eastern Pacific coast were investigated with CT scanning and electron microscopy. Ultrastructure of preecdysial and postecdysial cuticular layers was described in premoult, intramoult and postmoult animals. Cuticle is a flexible extracellular matrix connected to the epidermal cells through pore channels. During premoult epicuticle and exocuticle are formed and during intramoult and postmoult endocuticular lamellae are deposited and the cuticle is progressively constructed by thickening and mineralization. Cuticle permeability, flexibility and waterproofing capacity change accordingly. Elaboration of epicuticular scales connected to an extensive network of nanotubules, establish its anti-adhesive and hydrophobic properties. Labelling with gold conjugated WGA lectins on Tokuyashu thawed cryosections exposes differences in chitin content between exocuticle and endocuticle. Histochemical staining of cuticle shows presence of acidic carbohydrates/glycoconjugates and lipoproteins in epicuticular layer. Chitin microfibrils are formed at the microvillar border of epidermal cells with abundant Golgi apparatus and secretory vesicles. Numerous spherules associated with nanotubules were observed in the ecdysial space in intramoult animals. The mineral component of the cuticle as visualized with CT scanning indicates progressive mineral resorption from the posterior to the anterior half of the body in premoult animals, its translocation from the anterior to posterior part during intramoult and its progressive deposition in the posterior and anterior exoskeleton during postmoult. Cuticle of sea slaters is a unique biocomposite and biodynamic material constantly reconstructed during frequent moults, and adapted to specific physical and biotic conditions of the high intertidal rocky zone.
Keywords: cuticle ultrastructure, micro CT scanning, moult cycle, SEM, TEM, terrestrial isopods
Published in DiRROS: 23.07.2024; Views: 2; Downloads: 0
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5. Respiration rates in shallow lakes of different types : contribution of benthic microorganisms, macrophytes, plankton and macrozoobenthosJanusz Żbikowski, Tatjana Simčič, Franja Pajk, Małgorzata Poznańska-Kakareko, Tomasz Kakareko, Jarosław Kobak, 2019, original scientific article Abstract: The determination of the metabolic activity of organisms at various trophic levels is crucial for the proper assessment of the energy flow through the ecosystem, which is the basic process determining ecosystem functioning. We estimated the respiration rate in nine shallow, eutrophic lakes (macrophyte-dominated and phytoplankton-dominated) from north-eastern Poland. Respiratory carbon loss (RCL) through bottom microbial communities, macrophytes, plankton and macrozoobenthos was estimated by measuring the Electron Transport System activity. The shares of the particular ecosystem components in respiration processes differed among the lake types and seasons. The bottom microbial communities contributed most to the RCL (from 50% in the macrophyte-dominated lakes to 90% in the shallower phytoplankton-dominated lakes) except in macrophytes-dominated lakes in summer, where the macrophyte contribution prevailed (80%). The contribution of plankton was considerable only in the deeper phytoplankton-dominated lakes (20%). Macrozoobenthos was important (20%) only in the macrophyte-dominated lakes in spring and autumn. The RCL through bottom microbial communities was substantially higher in the shallow lakes (especially phytoplankton-dominated) than in deep, stratified eutrophic lakes. Shallow eutrophic lakes can be highly productive due to intensive organic matter mineralization at the bottom and rapid flow and cycling of carbon and nutrients resulting from their polymictic character.
Keywords: shallow lakes, ETS activity, respiratory carbon loss, abiotic parameters
Published in DiRROS: 23.07.2024; Views: 2; Downloads: 0
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7. A decline in molluscan carbonate production driven by the loss of vegetated habitats encoded in the Holocene sedimentary record of the Gulf of TriesteAdam Tomašových, Ivo Gallmetzer, Alexandra Haselmair, Darrell S. Kaufman, Borut Mavrič, Martin Zuschin, 2019, original scientific article Abstract: Carbonate sediments in non-vegetated habitats on the north-east Adriatic shelf are dominated by shells of molluscs. However, the rate of carbonate molluscan production prior to the 20th century eutrophication and overfishing on this and other shelves remains unknown because: (i) monitoring of ecosystems prior to the 20th century was scarce; and (ii) ecosystem history inferred from cores is masked by condensation and mixing. Here, based on geochronological dating of four bivalve species, carbonate production during the Holocene is assessed in the Gulf of Trieste, where algal and seagrass habitats underwent a major decline during the 20th century. Assemblages of sand-dwelling Gouldia minima and opportunistic Corbula gibba are time-averaged to >1000 years and Corbula gibba shells are older by >2000 years than shells of co-occurring Gouldia minima. This age difference is driven by temporally disjunct production of two species coupled with decimetre-scale mixing. Stratigraphic unmixing shows that Corbula gibba declined in abundance during the highstand phase and increased again during the 20th century. In contrast, one of the major contributors to carbonate sands – Gouldia minima – increased in abundance during the highstand phase, but declined to almost zero abundance over the past two centuries. Gouldia minima and herbivorous gastropods associated with macroalgae or seagrasses are abundant in the top-core increments but are rarely alive. Although Gouldia minima is not limited to vegetated habitats, it is abundant in such habitats elsewhere in the Mediterranean Sea. This live–dead mismatch reflects the difference between highstand baseline communities (with soft-bottom vegetated zones and hard-bottom Arca beds) and present-day oligophotic communities with organic-loving species. Therefore, the decline in light penetration and the loss of vegetated habitats with high molluscan production traces back to the 19th century. More than 50% of the shells on the sea floor in the Gulf of Trieste reflect inactive production that was sourced by heterozoan carbonate factory in algal or seagrass habitats.
Keywords: bioturbation, carbonate production, mollusca, northern Adriatic Sea, taphonomy, time averaging
Published in DiRROS: 23.07.2024; Views: 1; Downloads: 0
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8. Genetic characterisation of European mudminnow (Umbra krameri) populations from the Sava River systemSaša Marić, David Stanković, Radek Šanda, Marko Ćaleta, Srećko Čolić, Goran Šukalo, Aleš Snoj, 2019, original scientific article Abstract: Two new populations of the European mudminnow (Umbra krameri Walbaum, 1792) were discovered in the Sava River system, one in its middle part (Bosnia and Herzegovina) and the other in a tributary to the Kupa River (Croatia). The Croatian population is the most upstream mudminnow discovery in the Sava River system known to date. The genetic structure of the newly recorded mudminnow populations was examined using mitochondrial DNA and microsatellite loci. By adding these new populations to the analysis of the population genetic structure of mudminnow from the Sava River system, previously unresolved relationships between the populations from the upper and the lower Sava were clarified: the middle Sava populations were shown to be well outside the hybridisation zone with the Danubian clade, meaning the upstream boundary of this zone is confined to the lower Sava. The results also suggest that mudminnow populations in the Sava River system are less isolated than previously believed. Namely, intermediate gene-flow was detected when comparing the uppermost Sava population with the lower Sava populations. Taking these results into account, appropriate guidelines are proposed to preserve mudminnow populations from the Sava River system.
Published in DiRROS: 23.07.2024; Views: 2; Downloads: 0
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9. Y2O3-Al2O3 microsphere crystallization analyzed by electron backscatter diffraction (EBSD)Wolfgang Wisniewski, Anna Prnová, Peter Švančárek, Milan Parchovianský, Dušan Galusek, 2020, original scientific article Abstract: The crystallization of glass microspheres in the Y2O3–Al2O3-system produced from precursor powders of four different nominal compositions via flame synthesis is analyzed in detail by electron microscopy with a focus on electron backscatter diffraction (EBSD). Growth models are formulated for individual microspheres crystallized during flame synthesis as well as after an additional heat treatment step. 16 different types of crystallized bodies are cataloged for future reference. They are presented without regard for their relative occurrence; some are extremely rare but illustrate the possibilities of flame synthesis in the analyzed system. All three phases in the binary Y2O3–Al2O3-phase diagram (Y3Al5O12, YAlO3 and Y4Al2O9) and α-alumina are located by EBSD. Energy dispersive X-ray spectrometry results obtained from these microspheres show that their chemical composition can deviate from the nominal composition of the precursor powder. The multitude of differing microsphere types showing polygon and dendritic crystal growth as well as phase separation indicate that flame synthesis can lead to a wide variety of parameters during microsphere production, e.g. via irregular flight paths through the flame, contaminants or irregular cooling rates.
Keywords: Y2O3-Al2O3, microsphere crystallization, flame synthesis, EBSD
Published in DiRROS: 23.07.2024; Views: 0; Downloads: 0
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10. Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant developmentEdgardo Brigatti, Rubén González, Anamarija Butković, Mark Paul Selda Rivarez, Santiago F. Elena, 2020, original scientific article Abstract: Growth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.
Published in DiRROS: 23.07.2024; Views: 2; Downloads: 0
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