1. Learning deep representations of enzyme thermal adaptationGang Li, Filip Buric, Jan Zrimec, Sandra Viknander, Jens Nielsen, Aleksej Zelezniak, Martin K. M. Engqvist, 2022, izvirni znanstveni članek Povzetek: Temperature is a fundamental environmental factor that shapes the evolution of organisms. Learning thermal determinants of protein sequences in evolution thus has profound significance for basic biology, drug discovery, and protein engineering. Here, we use a data set of over 3 million BRENDA enzymes labeled with optimal growth temperatures (OGTs) of their source organisms to train a deep neural network model (DeepET). The protein-temperature representations learned by DeepET provide a temperature-related statistical summary of protein sequences and capture structural properties that affect thermal stability. For prediction of enzyme optimal catalytic temperatures and protein melting temperatures via a transfer learning approach, our DeepET model outperforms classical regression models trained on rationally designed features and other deep-learning-based representations. DeepET thus holds promise for understanding enzyme thermal adaptation and guiding the engineering of thermostable enzymes. Ključne besede: bioinformatics, deep neural networks, enzyme catalytic temperatures, optimal growth temperatures, protein thermostability, transfer learning Objavljeno v DiRROS: 17.07.2024; Ogledov: 152; Prenosov: 125
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2. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endospermShuang Zhang, Arindam Ghatak, Mitra Mohammadi Bazargani, Hannes Kramml, Fujuan Zang, Shuang Gao, Živa Ramšak, Kristina Gruden, Rajeev K. Varshney, Dong Jiang, Palak Chaturvedi, Wolfram Weckwerth, 2023, izvirni znanstveni članek Povzetek: The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes. Ključne besede: wheat, proteomics and metabolomics, aleurone, sub-aleurone, starchy endosperm, endosperm transfer cells Objavljeno v DiRROS: 15.07.2024; Ogledov: 149; Prenosov: 131
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3. An experimental apparatus for bench-scale fire testing using electrical heating padsAleksandra Seweryn, Andrea Lucherini, Jean-Marc Franssen, 2024, izvirni znanstveni članek Povzetek: This research study concerns an experimental, budget-friendly, electricity- powered apparatus for bench-scale fire testing. The apparatus consists of various elements, of which the most important are ceramic heating pads, used to impose heat fluxes on exposed surfaces of specimens. The test method allows to control the heating pads’ temperature and to adjust the distance between the heating pads and the specimen to obtain well-defined heat fluxes up to 50–60 kW/m2. Higher heat fluxes and temperatures can be obtained by setting the heating pads in full power mode, with or without the use of a thermal shield, which can lead to heat fluxes up to 150 kW/m2. The heating and thermal boundary conditions imposed by the apparatus are characterised and discussed, and the thickness of the convective boundary layer at the heating pads’ surface is estimated significantly lower than in the case of gas- fired radiant panels. The performance of the apparatus is analysed for various conditions: controlling the temperature of the heating pads, in an open environment or with the presence of thermal shields, and in full power mode. A few examples of application of the apparatus to fire test typical construction materials (steel and glass) are also presented. These results emphasise the well-defined heating conditions in temperature-controlled mode. The study finally discusses the advantages and limitations of the apparatus, as well as many possibilities of future applications and improvement for future research studies. Ključne besede: radiant panels, fire testing, heat transfer, heat flux, electrical heating pads, thermal boundary conditions Objavljeno v DiRROS: 15.04.2024; Ogledov: 304; Prenosov: 739
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4. A coupled convective-diffusive model of heat transfer and melt-pool dynamics in additive manufacturingTijan Mede, Matjaž Godec, 2024, elaborat, predštudija, študija Ključne besede: additive manufacturing, selective laser melting, laser powder-bed fusion, melt-pool, heat transfer, convection Objavljeno v DiRROS: 05.04.2024; Ogledov: 342; Prenosov: 0 |
5. Numerical heat transfer model for swelling intumescent coatings during heatingAndrea Lucherini, Juan P. Hidalgo, Jose L. Torero, Cristian Maluk, 2023, izvirni znanstveni članek Povzetek: This research study presents a heat transfer model aimed at estimating the thermal and physical response of intumescent coatings. The numerical model is inspired by the outcomes of an experimental study focused on analysing the insulating effectiveness of a commercial intumescent coating for a range of heating conditions and initial coating thickness. The model solves the one-dimensional heat conduction problem using the finite-difference Crank-Nicolson method, and it assumes that the effectiveness of intumescent coatings is mainly dependent on their ability to develop swelled porous char. The coating swelling is implemented in the model by adopting an approach based on expanding the mesh representing the physical domain in proximity to the substrate-coating interface. The model described herein offers researchers and engineers a tool to estimate the heat transfer of swelling intumescent coatings (i.e. in-depth thermal gradient). Outcomes of the analysis shown herein demonstrate that the heat conduction within intumescent coatings is governed by the physical coating swelling and the thermal conditions at the coating-substrate interface. The numerical model shows that its accuracy is highly influenced by the coating thickness ahead of the reaction zone. Consequently, the coating swelling rate plays a key role, while the thermo-physical properties of the intumescent coating have a secondary effect. According to its assumptions, the model defines a quasi-steady-state thermal problem: it is more accurate for conditions close to steady-state (e.g. high heat fluxes), but it loses accuracy for cases characterised by transient phenomena (e.g. phases prior to the onset of swelling and low heat fluxes). Ključne besede: intumescent coatings, heat transfer, numerical model, swelling, fire safety Objavljeno v DiRROS: 08.01.2024; Ogledov: 390; Prenosov: 65
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6. The status and role of genetic diversity of trees for the conservation and management of riparian ecosystems : a European experts' perspectiveFilip Alimpić, Jelena Milovanović, Remigiusz Pielech, Georgi Hinkov, Roland Jansson, Simon Dufour, Marcin Beza, Nebi Bilir, Luis Santos del Blanco, Gregor Božič, 2022, izvirni znanstveni članek Povzetek: Riparian vegetation supports high biodiversity providing many services and is, therefore, an important landscape element. Riparian ecosystems are subject to numerous pressures leading to population decline and genetic erosion of riparian plants. This may have cascading effects at various ecosystem levels, including decreasing ecosystem services, so identifying the current status of genetic diversity of riparian tree species is vital to improve the effectiveness of restoration efforts. We aimed to elicit expert views on the status and importance of genetic diversity of tree species, and conservation needs across European riparian ecosystems. Sharing of such information among researchers, managers and policymakers has the potential to enhance ecological restoration and management of riparian ecosystems. We identified experts in riparian genetic resources conservation and management across Europe. These included stakeholders with different perspectives, ranging from researchers to practitioners. We designed a set of questionnaires where our identified experts were asked to answer questions related to the status and conservation of genetic diversity of riparian tree species in their respective countries. Specifically, we asked about societal awareness, legislative tools, good practices and conservation or restoration projects accounting for intraspecific genetic diversity and differentiation of tree species in riparian ecosystems. Questionnaire responses were analysed and discussed in light of the scientific literature to define needs and priorities related to the management and conservation of genetic diversity of riparian tree species. The experts recognized that a combination of in situ and ex situ measures and/or integrative conservation of riparian ecosystems is the most appropriate option for conserving the genetic diversity of riparian tree species. Simultaneous application of conservation measures at the level of priority species, identified by experts, and protection of riparian areas are required. Synthesis and applications. This study revealed the importance of recognizing the ecological processes that shape the genetic diversity of riparian tree species in hydrographic networks (dendritic spatial configuration, specific patterns of gene flow among riparian populations, fragmentation of river by dams) but also the need to overcome socio-economic barriers, such as lack of policy priority, deficiency in funding and weak legislation framework. Ključne besede: biodiversity conservation, genetic erosion, genetic resources conservation, knowledge transfer, management, riparian genetic diversity, vegetation Objavljeno v DiRROS: 08.12.2022; Ogledov: 638; Prenosov: 410
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7. Surprising drought tolerance of Fir (Abies) species between past climatic adaptation and future projections reveals new chances for adaptive forest managementCsaba Mátyás, František Beran, Jaroslav Dostál, Jiří Čáp, Martin Fulín, Monika Vejpustková, Gregor Božič, Pál Balázs, Josef Frýdl, 2021, izvirni znanstveni članek Povzetek: esearch Highlights: Data of advanced-age provenance tests were reanalyzed applying a new approach, to directly estimate the growth of populations at their original sites under individually generated future climates. The results revealed the high resilience potential of fir species. Background and Objectives: The growth and survival of silver fir under future climatic scenarios are insufficiently investigated at the xeric limits. The selective signature of past climate determining the current and projected growth was investigated to analyze the prospects of adaptive silviculture and assisted transfer of silver fir populations, and the introduction of non-autochthonous species. Materials and Methods: Hargreaves% climatic moisture deficit was selected to model height responses of adult populations. Climatic transfer distance was used to assess the relative drought stress of populations at the test site, relating these to the past conditions to which the populations had adapted. ClimateEU and ClimateWNA pathway RCP8.5 data served to determine individually past, current, and future moisture deficit conditions. Besides silver fir, other fir species from South Europe and the American Northwest were also tested. Results: Drought tolerance profiles explained the responses of transferred provenances and predicted their future performance and survival. Silver fir displayed significant within-species differentiation regarding drought stress response. Applying the assumed drought tolerance limit of 100 mm relative moisture deficit, most of the tested silver fir populations seem to survive their projected climate at their origin until the end of the century. Survival is likely also for transferred Balkan fir species and for grand fir populations, but not for the Mediterranean species. Conclusions: The projections are less dramatic than provided by usual inventory assessments, considering also the resilience of populations. The method fills the existing gap between experimentally determined adaptive response and the predictions needed for management decisions. It also underscores the unique potential of provenance tests. Ključne besede: climate change, common garden, provenance test, silver fir, grand fir, Balkan firs, drought stress, resilience, climate transfer distance, adaptation Objavljeno v DiRROS: 05.07.2021; Ogledov: 1107; Prenosov: 687
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9. Bioinformatic analysis reveals archaeal tRNA sup [Tyr] and tRNA sup [Trp] identities in bacteriaTakahito Mukai, Noah M. Reynolds, Ana Crnković, Dieter Söll, 2017, izvirni znanstveni članek Ključne besede: aaRS, evolution, genetic code, lateral gene transfer, tRNA Objavljeno v DiRROS: 07.05.2020; Ogledov: 1909; Prenosov: 1154
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10. RNA-dependent cysteine biosynthesis in bacteria and archaeaTakahito Mukai, Ana Crnković, Takuya Umehara, Natalia N. Ivanova, Nikos C. Kyrpides, Dieter Söll, 2017, izvirni znanstveni članek Ključne besede: amino acyl-tRNA synthetases, archaea, archaeal proteins, bacteria, computational biology, crystallography, X-ray, genetic code, genome, archaeal, genome, bacterial, phosphoserine, protein binding, protein biosynthesis, RNA, archaeal, RNA, bacterial, RNA, transfer, amino acyl, RNA, transfer, cys, sulfur/metabolism, biochemistry, bioinformatics, cysteine biosynthesis, genetic code, translation Objavljeno v DiRROS: 07.05.2020; Ogledov: 1949; Prenosov: 1417
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