1,844 research outputs found
Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba
No full textArchaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA.Peer reviewe
Natural variation of response to glyphosate in Sinapis alba (Brassicaceae): Physiological effects, shikimate accumulation and genetic mechanisms
No full text15 Pags.- 7 Figs.- 2 Tabls. Data Availability Statement: The datasets generated and/or analyzed during the current study are available in the Zenodo Repository https://doi.org/10.5281/zenodo.15697367 © 2025 The Author(s). This is an open access article under the terms of the Creative Commons Attribution License.Glyphosate is the most widely used herbicide worldwide, and glyphosate-resistant weeds have increased globally. Resistance mechanisms, including target-site resistance (TSR) and non-target-site resistance (NTSR), are well documented, but their extent and importance are poorly understood among biotypes. This study examines the natural variation in glyphosate sensitivity and its genetic basis in white mustard (Sinapis alba L.) across 192 accessions in Southern Spain. We conducted a multi-population screening to evaluate plant performance, shikimate accumulation, survival and yield under glyphosate exposure and analysed the spatial response pattern. We also assessed the expression of two genes linked to glyphosate resistance, EPSPS and ABCC8, sequenced EPSPS to detect potential mutations and quantified its copy number. Results show glyphosate significantly reduces physiological parameters, with a 90% decrease in photosynthetic rate, a 22% reduction in chlorophyll concentration and a 38% decrease in specific leaf area. However, 32% of accessions survived and produced seeds under glyphosate exposure (1598 g.a.e. ha−1) in the vegetative stage. Survivors accumulated 13% less shikimate, indicating a reduced glyphosate effect on the shikimate pathway. Overexpression of the NTS ABCC8 gene was the most common mechanism in 39% of non-susceptible accessions. Yet, about 20% of survivors were not linked to EPSPS duplication or overexpression of EPSPS or ABCC8, suggesting other genetic mechanisms may contribute to glyphosate resistance in S. alba. Resistant phenotypes were widely dispersed, not confined to specific areas, highlighting the potential role of gene flow in the evolution of herbicide response in S. alba. Our study suggests that the plant resistance to glyphosate may arise from multiple and non-exclusive genetic mechanisms.This study was supported by P18-RT-2834 PAIDI 2020, Junta de Andalucia and Ref. PREDOC_01971 (PAIDI 2020).Peer reviewe
Genome Assembly and Annotation of <i>Populus alba</i> '<i>Berolinensis</i>' L.
No full textPopulus alba 'Berolinensis', a superior hybrid triploid material for studying the genomic mechanisms in heterosis of polyploid. In this project, we established a high-quality assembly of Populus alba 'Berolinensis', and found the stress-related gene sequence differences between its three haploid genomes, which provided a foundation for molecular breeding and deeper insights into polyploidy species.
This dataset has also been deposited in CNCB Genome Warehouse (BioProject: PRJCA009923), and NCBI GenBank (BioProject: PRJNA845083, PRJNA845082, and PRJNA845081). Raw sequencing data are available in the NCBI Sequence Read Archive (SRA) database (BioProject: PRJNA635615 and PRJNA721517). The gene expression information has been deposited into our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com).
Citation:
Chen, S., Yu, Y., Wang, X., Wang, S., Zhang, T., Zhou, Y., He, R., Meng, N., Wang, Y., Liu, W., Liu, Z., Liu, J., Guo, Q., Huang, H., Sederoff, R.R., Wang, G., Qu, G. and Chen, S. (2023), Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour. Accepted Author Manuscript. </p
Search for steady and flaring astrophysical neutrino point sources with the IceCube detector
No full textFür astrophysikalische Quellen, z.B. aktive galaktische Kerne, werden hochenergetische Neutrinoflüsse vorhergesagt. Neutrinos und Gammastrahlen werden in hadronischen Prozessen erzeugt, für die Protonen auf hohe Energien beschleunigt werden müssen. Da Neutrinos nur schwach wechselwirken und nicht von Magnetfeldern abgelenkt werden können, bleiben Flussstärken und ihre Richtung erhalten. IceCube, ein Kubikkilometer-Detektor der sich am Südpol befindet, kann solche Neutrinos nachweisen. In dieser Arbeit wurden Daten zweier Teilkonfigurationen IceCubes (22 und 40 Trossen) ausgewertet. Die Daten, die zwischen 2007 und 2009 gesammelt wurden, bestehen hauptsächlich aus atmosphärischen Myon-Neutrinos, die im Nordhimmel erzeugt wurden und hochenergetischen atmosphärischen Myonen aus dem Südhimmel. Eine zeitunabhängige Analyse, die nach Neutrino-Punktquellen im Nordhimmel sucht, wurde mit einem sensitivitäts-optimierten Datensatz von IceCube-22 durchgeführt. Die ganze Hemisphäre und eine Liste ausgewählter Quellen wurden analysiert, wobei kein Hinweis auf extraterrestrische Neutrino-Signale gefunden wurde. Um das Entdeckungspotenzial für eine variable Quelle zu erhöhen, wurde eine nicht-getriggerte zeitabhängige Analyse entwickelt. Diese Suche ist durch Neutrino-Photon-Korrelationen und Gammastrahlung-Ausbrüche kosmischer Objekte motiviert, jedoch wurden nur Neutrino-Daten verwendet. Ein grosser Bereich möglicher Strahlungsausbruchsdauer wurde abgedeckt. Die gebinnte Methode wurde zu einer ungebinnten Likelihood-Methode erweitert, so dass die Ergebnisse um 5-25% verbessert werden konnten. Auswahlkriterien für eine Liste zeitlich veränderlicher astrophysikalischer Quellen vom ganzen Himmel wurden für IceCube-22 und IceCube-40 entwickelt. Zum ersten Mal wurde eine zeitabhängige Suchmethode im Südhimmel benutzt. Es konnten keine Ereignisüberschüsse über dem Untergrund festgestellt werden. Demzufolge wurden obere Grenzen für Neutrinoflüsse aus diesen Quellen berechnet.High energy neutrino astronomy relies on the predictions of neutrino fluxes coming from astrophysical objects, for example active galactic nuclei. In these models, neutrinos and gamma-rays are produced in hadronic processes, which require the acceleration of protons to very high energies. Since neutrinos hardly interact and travel towards Earth undeflected by magnetic fields, they can point back to their sources. IceCube, located at the South Pole, is a large volumen detector for high energy neutrinos. In this work, data from two partial configurations of IceCube (22 and 40 strings) are analyzed. The data cover 651 days, from 2007 to 2009, and consist mostly of atmospheric muon neutrinos in the Northern sky and high energy atmospheric muons in the Southern sky. A time integrated search for neutrino point sources in the Northern sky was developed and applied to an event sample obtained for the best sensitivity, with IceCube 22-string. The search was performed on pre-selected sources and the whole hemisphere was scanned. No evidence of a neutrino signal was found. In order to enhance the flare detection probability, an untriggered time dependent search that looks for neutrino events clustering in time from specific sources in the entire sky was developed. This search was motivated by neutrino-photon correlations and the observations of flaring objects in gamma-rays, but focuses only on the neutrino data, covering a wide range of possible flare durations. The search method was expanded from a binned approach to a newly developed unbinned likelihood method, improving the results by 5-25%. Moreover, for the first time the Southern sky was analyzed with a time dependent method. A source selection criteria was developed defining two lists of variable astrophysical sources, for IceCube 22 and 40-string. The results were compatible with background fluctuations for all sources tested. Therefore, upper limits on the neutrino fluence from these sources are presented
A ALBA e a luta pela hegemonia no continente americano: uma topologia do discurso bolivariano
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas. Programa de Pós-graduação em Sociologia PolíticaO objetivo da dissertação é analisar o movimento bolivariano, liderado pela Venezuela, enquanto projeto de construção de uma nova hegemonia na América Latina e o Caribe. Tal projeto se constrói discursivamente em oposição à histórica hegemonia pan-americana liderada pelos Estados Unidos (EUA). Para isso é estudada a ALBA (Aliança Bolivariana para os Povos de nossa América) como organização internacional que facilita a alineação de países e sociedades latino-americanos em relação ao movimento bolivariano, gerando novas modalidades de construção de sentido, assim como novas vias e regras de relacionamento internacional. A pesquisa analisa os discursos de mandatários nas reuniões de Cúpula da ALBA, e, apelando à teoria do discurso de Ernesto Laclau, identifica nesse conjunto os três passos previstos pelo autor na configuração de um desafio hegemônico: (1) o estabelecimento de um antagonismo face ao imperialismo dos EUA que é identificado como o poder hegemônico institucionalizado, e a dicotomização do espaço social americano através da construção de uma fronteira entre esse poder e o resto da comunidade (América Latina e o Caribe); (2) a articulação contingente entre diversas demandas sociais, características da América Latina e do Caribe, cuja insatisfação é atribuída ao imperialismo dos EUA; e (3) a formação de um campo popular, através da expressão positiva dessas demandas numa nova identidade, no caso a identidade bolivariana. A pesquisa conclui que o movimento bolivariano consegue gerar elementos para permitir uma nova lógica de construção de sentido, configurando assim estruturalmente um campo de luta pela hegemonia. Porém, também são destacados vários problemas nessa tarefa, especialmente ligados à identificação de diversas unidades com o bolivarianismo.The dissertation research the Bolivarian Movement, headed by Venezuela, as a new hegemonic project, still under construction, at Latin America and the Caribbean. This hegemonic project is discursively constructed in opposition to the historic Pan American hegemony, led by the U.S. In this way, the Bolivarian Alliance for the Peoples of Our America (ALBA) is approached as an international organization that seeks to align the Latin American countries and societies behind the Bolivarian Movment. The ALBA generates new ways of sense-making, as well as new norms of international relations. The research analyzes the speeches at the ALBA's presidential summits, using the Ernesto Laclau's Discourse Theory, and identifying the three steps proposed by this author to the hegemonic construction: Firstly, the establishment of an antagonism against U.S. imperialism and the dicotomization of the hemispheric social space, through the definition of a boundary between the powerful country and the rest of continental community (Latina America and the Caribe). Secondly, the contingent articulation of a variety of social demands, which dissatisfaction are ascribed to the U.S. imperialism. Thirdly, the formation of a new popular field, through the positive expression on a new identity of this unified set of demands, in this case the Bolivarian identity. The dissertation concludes that the Bolivarian movement manages a new logic of sense-making, and therefore places the hegemonic struggle in a new structural field. However, it also identified some problems on this task, particularly in the difficulty to construct a Bolivarian identity shared by various social unities (countries, societies and social sectors)
Coherent J / ψ and {\uppsi '} ψ ′ photoproduction at midrapidity in ultra-peripheral Pb–Pb collisions at s NN = 5.02 TeV
No full textAbstract The coherent photoproduction of J / ψ and {\uppsi '} ψ ′ mesons was measured in ultra-peripheral Pb–Pb collisions at a center-of-mass energy s NN = 5.02 TeV with the ALICE detector. Charmonia are detected in the central rapidity region for events where the hadronic interactions are strongly suppressed. The J / ψ is reconstructed using the dilepton ( l + l - ) and proton–antiproton decay channels, while for the {\uppsi '} ψ ′ the dilepton and the l + l - π + π - decay channels are studied. The analysis is based on an event sample corresponding to an integrated luminosity of about 233 μ b - 1 . The results are compared with theoretical models for coherent J / ψ and {\uppsi '} ψ ′ photoproduction. The coherent cross section is found to be in a good agreement with models incorporating moderate nuclear gluon shadowing of about 0.64 at a Bjorken-x of around 6 × 10 - 4 , such as the EPS09 parametrization, however none of the models is able to fully describe the rapidity dependence of the coherent J / ψ cross section including ALICE measurements at forward rapidity. The ratio of {\uppsi '} ψ ′ to J / ψ coherent photoproduction cross sections was also measured and found to be consistent with the one for photoproduction off protons
Genetic Relationships and Reproductive Traits of Romanian Populations of Silver Fir (Abies alba): Implications for the Sustainable Management of Local Populations
No full text[EN] Assessment of the diversity of reproductive traits and genetic variation is of great relevance to the conservation of genetic resources and management of silver fir (Abies alba) populations. We have evaluated reproductive characteristics associated with female cones and seed morphology, as well as seed germination after subjecting seeds to five storage methods, in nine Romanian populations of A. alba. The genetic diversity of the populations was assessed with 12 polymorphic simple sequence repeat (SSR) markers. We detected significant differences between populations for all reproductive traits and considerable differences in seed germination and storage methods; seed storage in wet sand was the method resulting in the highest germination in all populations. Genomic SSRs (gSSRs) were more informative on average than expressed sequence tag SSRs (EST-SSRs) in the populations studied. The nine populations were genetically diverse, with an average number of alleles (N) per SSR locus between 3.50 and 4.83. The observed heterozygosity (Ho) in the nine populations was always lower than the expected heterozygosity (He), which resulted in values of the inbreeding coefficient (Fis) between 0.261 and 0.709. Genetic distances between populations ranged between 0.077 and 0.410. The cluster analysis based on genetic distances did not group accessions according to their geographical proximity, and despite a positive trend, the correlation between geographic and genetic distances was non-significant. The results of an analysis of molecular variance (AMOVA) revealed that only 9.1% of the total molecular variance is attributable to differences between populations. This low degree of genetic differentiation between populations is confirmed by the intermingling of individuals of different populations in a principal coordinate analysis (PCoA). We found evidence of a positive relationship between He and germination, as well as a negative one between Fis and germination, suggesting that populations with low diversity and high consanguinity may have a reduced fitness and long-term viability. The results are relevant for the conservation and management of local genetic resources and populations, as well as for reforestation programmes of silver fir.The publication was supported by funds from the National Research Development Projects to Finance Excellence (PFE)-37/2018-2020 granted by the Romanian Ministry of Research and Innovation. The first author (I.M.T.M.) is thankful to UPV (Valencia) and the Erasmus+ mobility programme, financed by the European Commission, for her scholarship in UPV. The research was partially supported by the Advanced Horticultural Research Institute of Transylvania (ICHAT), University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca (USAMVCN), and Polytechnic University of Valencia (UPV). Mariola Plazas is grateful to Generalitat Valenciana and Fondo Social Europeo for a post-doctoral grant (APOSTD/2018/014).Todea Morar, IM.; Rensen, S.; Vilanova Navarro, S.; Boscaiu, M.; Holonec, L.; Sestras, AF.; Vicente, O.... (2020). Genetic Relationships and Reproductive Traits of Romanian Populations of Silver Fir (Abies alba): Implications for the Sustainable Management of Local Populations. Sustainability. 12(10):1-15. https://doi.org/10.3390/su12104199S1151210Dering, M., Sękiewicz, K., Boratyńska, K., Litkowiec, M., Iszkuło, G., Romo, A., & Boratyński, A. (2014). Genetic diversity and inter-specific relations of western Mediterranean relic Abies taxa as compared to the Iberian A. alba. 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Author Correction: SREBP1 drives keratin-80-dependent cytoskeletal changes and invasive behavior in endocrine-resistant ERα breast cancer (Nature Communications, (2019), 10, 1, (2115), 10.1038/s41467-019-09676-y)
No full textThis Article contained an error in the name of the author Alba Rodríguez-Meira, which was incorrectly given as Alba Rodríguez Meira. These errors have been corrected in the PDF and HTML versions of the article. © 2019, The Author(s)
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