Vegetation of the Dolines in Mecsek Mountains (South Hungary) in relation to the Local Plant Communities

This paper deals with the forest vegetation of the lower part of the dolines in Mecsek Mts. (South Hungary). In order to char-acterize this vegetation type, samples were compared to the 6 plant communities occurring in the neighbourhood of the dolines. Considering the vegetation texture and species com-position, the vegetation of the dolines resembles mainly the extrazonal beechwoods (Helleboro odori-fagetum) and local ravine forests (Scutellario altissimae-Aceretum) that preserve several mountain, subatlantic relict species in this area. Our study revealed that the plant communities characteristic of the karst surface of Western Mecsek are arranged along a moisture and nutrient gradient. In this system, the habitat conditions of the dolines are similar to those of the beech forests and the lo-cal ravine forests, fresh and relatively rich in nutrients. In the karst, dominated by oak-hornbeam and beech forests, effects of the thermal inversion are the most spectacular where beech forests follow turkey oak-sessile oak forests and oak-hornbeam forests on the lower part of the doline slopes. The described vegetation type of these depressions is developed by edafic fac-tors; its identification as a separate association is not supported by the analyses

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.Fil: Quaglia, Federica. Università di Padova; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Mészáros, Bálint. European Molecular Biology Laboratory; AlemaniaFil: Salladini, Edoardo. Università di Padova; ItaliaFil: Hatos, András. Università di Padova; ItaliaFil: Pancsa, Rita. Research Centre for Natural Sciences; HungríaFil: Chemes, Lucia Beatriz. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Pajkos, Mátyás. Eötvös Loránd University; HungríaFil: Lazar, Tamas. Vlaams Instituut voor Biotechnology; Hungría. Vrije Unviversiteit Brussel; BélgicaFil: Peña Díaz, Samuel. Universitat Autònoma de Barcelona; EspañaFil: Santos, Jaime. Universitat Autònoma de Barcelona; EspañaFil: Ács, Veronika. Research Centre for Natural Sciences; HungríaFil: Farahi, Nazanin. Vlaams Instituut voor Biotechnology; Bélgica. Vrije Unviversiteit Brussel; BélgicaFil: Fichó, Erzsébet. Research Centre for Natural Sciences; HungríaFil: Aspromonte, Maria Cristina. Università di Padova; Italia. Città della Speranza Pediatric Research Institute; ItaliaFil: Bassot, Claudio. Stockholms Universitet; SueciaFil: Chasapi, Anastasia. Centre for Research & Technology Hellas; GreciaFil: Davey, Norman E.. Chester Beatty Laboratories; Reino UnidoFil: Davidović, Radoslav. University of Belgrade; SerbiaFil: Laszlo Holland, Alicia Verónica. European Molecular Biology Laboratory; Alemania. Research Centre for Natural Sciences; HungríaFil: Elofsson, Arne. Stockholms Universitet; SueciaFil: Erdős, Gábor. Eötvös Loránd University; HungríaFil: Gaudet, Pascale. Swiss Institute of Bioinformatics; SuizaFil: Giglio, Michelle. University of Maryland School of Medicine; Estados UnidosFil: Glavina, Juliana. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Iserte, Javier Alonso. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Iglesias, Valentín. Universitat Autònoma de Barcelona; EspañaFil: Kálmán, Zsófia. Pázmány Péter Catholic University; HungríaFil: Lambrughi, Matteo. Danish Cancer Society Research Center; DinamarcaFil: Leonardi, Emanuela. Università di Padova; Italia. Pediatric Research Institute Città della Speranza; ItaliaFil: Rodriguez Sawicki, Luciana. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Transitions between community complexes: a case study analysing gradients through mountain ridges in South Hungary

The study of boundaries is a recurring theme in ecology. However, boundaries have been examined mainly on fine scales (between communities) and on coarse scales (between biomes), while boundaries of intermediate scales (e.g. between community complexes) are quite neglected. In this study, we analysed boundaries between mesic and xeric community complexes in a sub- mediterranean karst area of South Hungary. We applied the moving split window (MSW) technique for boundary analysis. First, since the behaviour of MSW concerning complex vegetation patterns is not fully understood, we prepared artificial datasets (simulated communities) to test its capacities. Second, we established north-south oriented belt transects across mountain ridges of the Villány Mts, and investigated the transition between the community complexes of differently exposed slopes. Using MSW, we were able clearly to distinguish between transitional zones and zones that do not represent real transitions: peaks in the Z-score profile of MSW merge only in the case of transitional zones. Moreover, we found that peaks merge depending on the independence (distinctness) of the transitional zone: when it is distinct, peaks merge only at the largest window widths. In the Villány Mts, transitions seem to occur mostly in the grasslands north of the ridges. We demonstrated that these grasslands can be regarded as boundaries between mesic and xeric complexes or as zones in their own right, with their own two boundaries. Interpretation depends upon the scale of observation

Constructing Big Trees from Short Sequences

The construction of evolutionary trees is a fundamental problem in biology, and yet methods for reconstructing evolutionary trees are not reliable when it comes to inferring accurate topologies of large divergent evolutionary trees from realistic length sequences. We address this problem and present a new polynomial time algorithm for reconstructing evolutionary trees called the Short Quartets Method which is consistent and which has greater statistical power than other polynomial time methods, such as Neighbor-Joining and the 3-approximation algorithm by Agarwala et al. (and the "Double Pivot" variant of the Agarwala et al. algorithm by Cohen and Farach) for the L1-nearest tree problem. Our study indicates that our method will produce the correct topology from shorter sequences than can be guaranteed using these other methods

The Short Quartet Method

Reconstructing phylogenetic (evolutionary) trees is a major research problem in biology, but unfortunately the current methods are either inconsistent somewhere in the parameter space (and hence do not reconstruct the tree even given unboundedly long sequences), have poor statistical power (and hence require extremely long sequences on large or highly divergent trees), or have computational requirements that are excessive. We describe in this paper a new method, which we call the Short Quartet Method, for inferring evolutionary trees. The Short Quartet Method has great statistical power, is provably consistent throughout the parameter space, and uses only polynomial time. We present the results of experimental studies based upon simulations of sequence evolution that demonstrate its greater statistical power than neighbor-joining [33], perhaps the most popular method for phylogenetic tree inference among molecular biologists

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

International audienceThe Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure