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The Leishmania ribosome: more than passive mRNA translating machinery
No full textWhile the central dogma of molecular biology describes how genetic information flows, gene expression is also affected by epigenetic and epitranscriptomic processes. A recent report by Rajan et al. demonstrates how pseudouridylation of a Leishmania ribosomal rRNA affects the expression of particular proteins: an example of epitranslatomic control.I thank the Spanish Ministerio de Ciencia, Innovación (MICINN), Agencia Estatal de Investigación (AEI), grant number PID2020-117916RB-I00/AEI/10.13039/501100011033, and Instituto de Salud Carlos III, grant CB21/13/00018 (CIBERINFEC) for support
Curvas de infiltración acumulativa medidas en columnas de dos capas formadas por suelos humectables [Dataset]
No full text[ENG] The dataset is structured in a single Excel file with three sheets, each containing raw data of cumulative infiltration curves followed by gravity drainage. In each sheet, the first row labels the different infiltration curves. The infiltration curves are defined by pairs of columns, where the first column denotes time (in seconds) and the second column of each pair corresponds to the cumulative infiltration data (in centimeters). Each pair of columns represents a different material, distinguished by color-coded headings for clarity.
The first sheet, labelled Synthetic Infiltration Curves, contains the infiltration curves followed by gravity drainage simulated with HYDRUS-1D on 5 cm high columns with different materials. These include homogeneous columns of sandy loam (SL) and loam (L) as well as columns with different soil configurations and geometries. For example, 1 cm SL-4 cm Si means a 1 cm layer of sandy loam over a 4 cm layer of silt (Si).
The second sheet, entitled Laboratory Infiltration Curves, contains two cumulative infiltration curves measured in laboratory in two different columns of 5 cm high. The columns consisted of a 2.5 cm layer of sand on top of a 2.5 cm of sieved loam soil, and the reverse configuration.
The third sheet, Undistub. cores inf. curves, shows the cumulative infiltration curves measured in undisturbed soil cores collected from forest soils coming from three different municipalities of Huesca-Spain.[ESP] El conjunto de datos está estructurado en un único archivo Excel con tres hojas, cada una de las cuales contiene datos brutos de curvas de infiltración acumulada seguidas de drenaje por gravedad. En cada hoja, la primera fila etiqueta el nombre de las diferentes curvas de infiltración. Las curvas de infiltración están definidas por pares de columnas, donde la primera columna denota el tiempo (en segundos) y la segunda columna de cada par corresponde a los datos de infiltración acumulada (en centímetros). Cada par de columnas representa un material distinto, que se distingue por un código de colores para mayor claridad.
La primera hoja, etiquetada Synthetic Infiltration Curves, contiene las curvas de infiltración seguidas del drenaje por gravedad simulado con HYDRUS-1D en columnas de 5 cm de altura con diferentes materiales. Éstas incluyen columnas homogéneas de suelo franco arenoso (SL) y suelo franco (L), así como columnas con diferentes configuraciones y geometrías de suelo. Por ejemplo, 1 cm SL-4 cm Si significa una capa de 1 cm de suelo franco arenoso sobre una capa de 4 cm de limo (Si).
La segunda hoja, titulada Laboratory Infiltration Curves, contiene dos curvas de infiltración acumulada medidas en laboratorio sobre dos columnas diferentes de 5 cm de altura. Las columnas consisten en una capa de 2,5 cm de arena sobre una capa de 2,5 cm de suelo franco tamizado, y la configuración inversa.
La tercera hoja, Undistub. cores inf. curves, muestra las curvas de infiltración acumulada medidas en testigos de suelo inalterados recogidos de suelos forestales procedentes de tres municipios diferentes de Huesca-España.This dataset is covered by a Creative Commons Licence Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).[ENG] The excel file includes a series of synthetic infiltration curves followed by gravity drainage simulated with HYDRUS-1D. These data correspond to infiltration curves generated in 5 cm high homogeneous columns of sandy loam (SL) and loam (L,) as well as, 5 cm high columns with different configurations of soils and geometries. For example, 1 cm SL-4 cm Si denotes a 1 cm layer of sandy loam overlying on a 4 cm layer of silt (Si).
The file also includes infiltration curves followed by gravity drainage measured on laboratory columns consisting of 2.5 cm of sand placed on a 2.5 cm layer of sieved loam soil, and the opposite configuration.
Finally, three infiltration curves measured in 5 cm columns of undisturbed soil are also included collected in forest soils.ESP] El archivo Excel incluye una serie de curvas de infiltración sintéticas seguidas de drenaje por gravedad simuladas con HYDRUS-1D. Estos datos corresponden a curvas de infiltración generadas en columnas homogéneas de 5 cm de altura con suelo franco arenoso (SL) y suelo franco (L), así como columnas de 5 cm de altura con diferentes configuraciones de suelo y geometrías. Por ejemplo, 1 cm SL-4 cm Si denota una capa de 1 cm de suelo franco arenoso sobre una capa de 4 cm de limo (Si).
El archivo también incluye curvas de infiltración seguidas de drenaje por gravedad medidas en columnas de laboratorio compuestas por 2,5 cm de arena sobre 2,5 cm de suelo franco tamizado, y la configuración opuesta.
Por último, también se incluyen tres curvas de infiltración medidas en columnas de 5 cm de suelo inalterado recogidas en suelos forestales.Proyecto RENURSE (TED2021-132406B-I00), financiado por el Ministerio de Ciencia e InnovaciónPeer reviewe
High-Temperature QCD Static Potential beyond Leading Order
No full textWe calculate the leading and next-to-leading corrections to the real-time QCD static potential in a high-temperature medium in the region where bound states transit from narrow resonances to wide ones. We find sizable contributions to both the real and the imaginary part of the potential. The calculation involves both loop diagrams calculated in the hard thermal loop effective theory and power corrections to the hard thermal loop Lagrangian calculated in QCD. We compare our results with recent lattice data and check the consistency of different methods used in lattice calculations. We also discuss the usefulness of our results to guide lattice inputs.We thank Peter Petreczky and Rasmus Larsen for providing the data of Refs. [51] and [16], respectively. M. E. C. acknowledges support by the Natural Sciences and Engineering Research Council of Canada under Grant No. SAPIN-2023-00023 and thanks ICCUB and ICE for hospitality. C. M. was supported by Ministerio de Ciencia, Investigación y Universidades (Spain) MCIN/AEI/10.13039/501100011033/ FEDER, UE, under Project No. PID2022-139427NB-I00, by Generalitat de Catalunya by Project No. 2021-SGR-171 (Catalonia), and also partly supported by the Spanish program Unidad de Excelencia Maria de Maeztu CEX2020-001058-M, financed by MCIN/AEI/10.13039/501100011033. J. S. acknowledges financial support from Grants No. 2017-SGR-929 and No. 2021-SGR-249 from the Generalitat de Catalunya and from Projects No. PID2022-136224NB-C21, No. PID2022-139427NB-I00, and No. CEX2019-000918-M from Ministerio de Ciencia, Innovación y Universidades.With funding from the Spanish government through the "María de Maeztu Unit of Excellence" accreditation (CEX2020-001058-M)Peer reviewe
Verbascum species as a new source of saffron apocarotenoids and molecular tools for the biotechnological production of crocins and picrocrocin
No full textCrocins are glucosylated apocarotenoids present in flowers and fruits of a few plant species, including saffron, gardenia, and Buddleja. The biosynthesis of crocins in these plants has been unraveled, and the enzymes engineered for the production of crocins in heterologous systems. Mullein (Verbascum sp.) has been identified as a new source of crocins and picrocrocin. In this work, we have identified eight enzymes involved in the cleavage of carotenoids in two Verbascum species, V. giganteum and V. sinuatum. Four of them were homologous to the previously identified BdCCD4.1 and BdCCD4.3 from Buddleja, involved in the biosynthesis of crocins. These enzymes were analyzed for apocarotenogenic activity in bacteria and Nicotiana benthamiana plants using a virus-driven system. Metabolic analyses of bacterial extracts and N. benthamiana leaves showed the efficient activity of these enzymes to produce crocins using β-carotene and zeaxanthin as substrates. Accumulations of 0.17% of crocins in N. benthamiana dry leaves were reached in only 2 weeks using a recombinant virus expressing VgCCD4.1, similar to the amounts previously produced using the canonical saffron CsCCD2L. The identification of these enzymes, which display a particularly broad substrate spectrum, opens new avenues for apocarotenoid biotechnological production
Advanced fermentation techniques enhance dioxolanone type biopesticide production from Phyllosticta capitalensis
No full textThe obtained ITS1-5.8S-ITS2 sequence data was compared with these published in the NCBI (National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/) database using Basic Local Alignment Search Tool (nBLAST). This strain was identified by similarity with another P. capitalensis strain (GenBank accession MT649668). A sample of this fungus was deposited in CECT (Valencia, Spain) under the number 20914 in compliance with the Budapest Treaty. The datasets used in the current study are available from the corresponding author on reasonable request.In the current work, the production of dioxolanone and meroterpene type secondary metabolites under different fermentation conditions by the endophytic fungus Phyllosticta capitalensis (isolate YCC4) isolated from the leaves of the endemic plant Persea indica has been evaluated. Different techniques, such as microparticle-enhanced culture (MPEC: bentonite, talcum powder) and surface adhesion fermentation (SAF: metallic mesh and glass wool) were applied to the culture medium. Ethyl acetate extracts from different fermentations of the isolate YCC4 were analyzed for their content and revealed the following dioxolanone derivatives: metguignardic acid (1), guignardianone C (2), ethyl guignardate (3), guignardianone D (4) and phenguignardic acid methyl ester (5), and meroterpenes: guignardone A (6) and B (7), guignarenone C (8), guignarenone B (9) and guignardone I (10). Additionally, the biological activity of extracts was tested against the aphid Myzus persicae and the root-knot nematode Meloidogyne javanica. Our study revealed significant variations in the production of the target metabolites as well as notable differences in biopesticide activity influenced by the presence of inert supports. Overall, the findings indicate that glass wool (GW) is a high-performance material to improve the production of dioxolanone derivatives. These findings underscore the significance of innovative cultivation methods such MPEC and SAF as drivers to produce valuable secondary metabolites from fungal organisms.This work has been funded by grant PID2019-106222RB-C31 funded by MCIN. Jorge Rojas López-Menchero has been supported by a predoctoral contract associated to the project PID2019-106222RB-C31 funded by MCIN/AEI/https://doi.org/10.13039/501100011033 and FSE “El FSE invierte en tu futuro”.Peer reviewe
Isolation, identification, and application of zinc-solubilizing bacteria exhibiting beneficial traits to promote plant growth and metal uptake
No full textThis study was conducted to isolate and characterize zinc (Zn)-solubilizing, plant growth-promoting (PGP) bacterial strains from mine soils and evaluate their inoculation effects on the growth and Zn uptake of corn and Indian mustard. A total of 171 Zn-tolerant bacterial strains were isolated from the mine soils, out of which six strains showed a significant increase (P < 0.01) in Zn solubility in a sucrose-minimal salt low-phosphate liquid medium. This increase in solubility was accompanied by a significant decrease (P < 0.01) in the pH values of the medium. The Zn-solubilizing bacteria (ZSB) were found to exhibit multiple PGP traits. All the strains were found to produce varying amounts of indole acetic acid and siderophore. Additionally, four of the strains displayed the ability to solubilize phosphate. These strains also demonstrated resistance to heavy metals, salinity, and diverse pH ranges. Based on the 16S rRNA gene sequence analysis, it was determined that the Zn-solubilizing strains belonged to four genera: Bacillus, Paenibacillus, Klebsiella, and Brevibacterium. Corn plants grown in Zn-contaminated sand exhibited enhanced shoot growth and Zn accumulation after inoculation with the selected Zn-solubilizing PGP strains, namely Bacillus tequilensis YSP3 and Paenibacillus pabuli YSP148. The efficiency of the YSP3, YSP148, and YSP3+YSP148 consortium bacterial inocula was also demonstrated in enhancing growth and metal (Zn, Pb, and Cd) uptake of corn and Indian mustard grown in a metal-contaminated soil. The study thus suggests the ZSB could play an important role in remediating metal-contaminated lands through microbe-assisted phytoremediation approaches.This work was supported by grants from the Isfahan University of Technology, Iran (Grant Number: 29965) and the Agencia Estatal de Investigación (AEI), Spain (Grant Number: PID2021-125371OB-I00).Peer reviewe
Source apportionment of PM10 particles in the urban atmosphere using PMF and LPO-XGBoost
Full text linkAtmospheric particulate matter (PM), as a leading part of air pollution, affects health in many ways. Thus, identifying and quantifying the contribution of atmospheric particulate matter sources of PM is vital for developing effective air quality management strategies. Positive Matrix Factorization (PMF) is one of the most common methods for source apportionment. However, PMF has some limitations, particularly its assumption that each source contributes linearly. In reality, some sources may exhibit nonlinear behaviors, which can compromise the accuracy of source apportionment. This study introduces a Lung Performance Optimization-based XGBoost (LPO-XGBoost) model, which leverages adaptive optimization principles inspired by lung function to enhance classic PM source apportionment. We demonstrate the potential for efficient, real-time application of the LPO-XGBoost model across 21 monitoring sites in 6 European countries. Trained and validated on extensive environmental datasets, the model is capable of predicting major pollution sources, including road traffic, biomass burning, crustal, industrial, nitrate-rich particles, sulfate-rich particles, heavy fuel oil, and sea salt. It outperforms other machine learning models with an overall predictive coefficient of determination (r2 = 0.88). Notably, the model performs exceptionally well in predicting sources such as sea salt (r2 = 0.97) and biomass burning (r2 = 0.89), but shows lower accuracy for the sulfate-rich particles source (r2 = 0.75). Comparative analyses with models including Random Forest (RF), Support Vector Machine (SVM), and their LPO-enhanced variants confirm that LPO-XGBoost provides the most reliable performance in estimating pollution source contributions, offering scalability and robustness ideal for high-time-resolution observational data. This model has significant potential to support targeted air quality management strategies. Future research should focus on expanding key species measurements at monitoring sites, ensuring consistent temporal coverage, and optimizing the model for improved mixed-source predictions to strengthen its applicability in comprehensive urban air quality assessments.This study has been supported and been done by RI-URBANS project (Research Infrastructures Services Reinforcing Air Quality Monitoring Capacities in European Urban & Industrial Areas, European Union's Horizon 2020 research and innovation program, Green Deal, European Commission, contract 101036245). Furthermore, additional support has been received from State Key Laboratory of Resources and Environmental Information System, the National Natural Science Foundation of China (42407566, 42205099, 72441001), and the Chunhui Project Foundation of the Education Department of China (HZKY20220053), the Science Fund for Creative Research Groups of the National Natural Science Foundation of China (72221002) that carried out the ML implementation. Meanwhile, samples in France were collected within many research and Air Quality assessment programs, including the programs CARA (funded by the Ministry of Environment within the LCSQA), DECOMBIO, CAMERA, and QAMECS (all funded by Ademe), ACME and MIAI-Airquality (funded by University Grenoble Alpes), OPE – Andra (funded by Andra), and multiple fundings by Atmo AuRA, Atmo Sud, Atmo Grand Est, Atmo Haut de France, Atmo Normandie, for the sampling and analyses. We would like to express our deep thanks to many people in the AASQA France for the sampling of all these samples, and to people in several laboratories in France, including IGE, for the analyses of these samples. The University of Aveiro thanks the Foundation for Science and Technology (FCT) for funding CESAM (UID Centro de Estudos do Ambiente e do Mar + LAP/0094/2020). The University of Granada acknowledges the financial support of the Spanish Ministry of Science and Innovation through the project ELPIS PID2020-120015RB-I00. Samples in Switzerland were collected by the Swiss National Air Pollution Monitoring Network NABEL (BAFU/Empa).Peer reviewe
‘Megafire’—You May Not Like It, But You Cannot Avoid It
Full text linkThe data used in this study are openly available at zenodo.org: https://doi.org/10.5281/zenodo.14020711.Aim: The term ‘megafire’ is increasingly used to describe large fires worldwide. We proposed a size-based definition of megafire—fires exceeding 10,000 ha arising from single or multiple related ignition events. A recent perspective in Global Ecology and Biogeography argues against a size-based definition of megafire and suggest that the term is too emotive for scientific use. We highlight that many scientific terms originate from common terms. These terms are often defined once they enter the scientific lexicon, enhancing both scientific understanding and public communication. We argue that standardised definitions facilitate better prediction, preparation, and management of fire events. Location: Worldwide. Time Period: 2022–2023. Methods: We conducted an updated structured review of the term ‘megafire’ and its use and definition in the peer-reviewed scientific literature, collating definitions and descriptions and identifying the criteria frequently invoked to define the term. Results: We demonstrate an increase in the use of ‘megafire’ in the scientific literature since our original definition in 2022, with many studies adopting the > 10,000 ha size-based criterion. Main Conclusions: We contend that abandoning the term is neither practical, possible, nor beneficial. Instead, consistent usage underpinned by clear definitions is essential. Adopting a clear, size-based definition of megafire strengthens clarity and comparability across research and management practices globally. Precision in terminology is crucial for advancing research, improving communication, and informing effective fire management and policy.This work was supported by the Gulbali Institute, Charles Sturt University. Macquarie University Research Fellowship (MQRF). ‘Ramón y Cajal’ fellowship of the Spanish Ministry of Science and Innovation (RYC2022-036822-I).Peer reviewe
Eucalyptus cover as the primary driver of native forest bird reductions: Evidence from a stand-scale analysis in NW Iberia
No full text12 pages, 3 figures, 3 tables; Supplementary data associated with this article can be found in the online version at doi:10.1016/j.foreco.2025.122714.; Data will be made available on request.The rapid expansion of exotic eucalyptus plantations across the Iberian Peninsula, particularly in northwest Spain, where they now cover 30 % of the region's forested area, has profoundly transformed rural landscapes, raising serious concerns about its impact on native biodiversity. This study investigates the influence of structural and floristic attributes of eucalyptus plantations and native forests on forest bird communities, focusing on species abundance and occurrence at the stand level. We conducted point count surveys and vegetation assessments across 240 plots, applying Generalized Linear Models (GLMs) and multimodel inference (MMI) to identify key drivers of avian diversity. Vegetation structure and composition differed substantially between native forests and eucalyptus plantations. Bird species richness and abundance were significantly lower in eucalyptus plantations. The proportion of eucalyptus emerged as the strongest predictor of these reductions, likely due to the limited availability of key resources such as natural cavities and arthropods. Mature native trees were pivotal in supporting forest bird species, particularly those associated with mature forest ecosystems. In contrast, mature eucalyptus trees failed to serve as adequate surrogates for mature native trees, benefiting only a small subset of forest specialists. Similarly, the well-developed shrub layer in eucalyptus plantations provided limited support for generalist bird species. To mitigate biodiversity loss, we recommend integrating unmanaged retention strips within eucalyptus plantations to enhance habitat heterogeneity and structural diversity, ensuring critical resources for birds and other forest wildlife while balancing forestry productivity with conservation goals.This work was supported by EU Marie Skłodowska-Curie Action awarded to FIRE-ADAPT project no. 101086416 and by EU Horizon 2020 grant no. 101036926 to the TREEADS project. P.M.F. was supported by the Portuguese Foundation for Science and Technology (https://doi.org/10.54499/UIDB/04033/2020). Da.A. was supported by Agritech National Research Center, Next-Generation EU. A.R. is supported by the Spanish ‘Ramón y Cajal’ fellowship programme (RYC2022-036822-I)