Prisutnost brezovog potkornjaka bjelikara (Scolytus ratzeburgi) u Hrvatskoj

Bark beetles are one of the most important groups of forest pests and in recent years several bark beetle species have significantly impacted two biogeographic regions in Croatia. The Birch bark beetle (Scolytus ratzeburgi) is the only Scolytus species known to infest birch (Betula spp.) and is a potential threat to birch trees in Croatia but its presence has not been recorded for over 100 years. Here we review historical records of this species and examine several forest stands of Silver birch (B. pendula). The last published record of Birch bark beetle was from 1913 and entomological collections from Croatia only have specimens from neighboring countries. Examination of Silver birch forest stands discovered five new locations of Birch bark beetle with signs of its attack. This species in Croatia has a low population density in forests and urban areas. Impacts of this species may be minimal, but research on this bark beetle should not be neglected since it represents valuable part of entomofauna in Croatia. Further research in Croatia should target fungal relationships with this species in order to determine whether the bark beetle spreads tree pathogenic fungi. Assessment of possible long-term mortality trends across the southern range edge of Silver birch and the presence of the Birch bark beetle merits further attention.Potkornjaci su jedna od najvažnijih skupina šumskih štetnika, a u posljednjih nekoliko godina zabilježene su štete od istih u dvije biogeografske regije Hrvatske. Smrekov pisar (Ips typographus) na području alpinske i mediteranski potkornjak (Orthotomicus erosus) na području mediteranske regije ukazali su na njihovu važnost. Brezov potkornjak bjelikar (Scolytus ratzeburgi) je jedina vrsta iz roda Scolytus kojoj su domaćini vrste iz roda Betula spp. te kao takva može predstavljati potencijalnu opasnost u Hrvatskoj. Prisutnost ove vrste je vidljiva po rupicama na kori, ispod kojih se nalazi materinski hodnik (Slika 2), a mužjak i ženka se razlikuju po količini dlaka na prednjem dijelu glave te po izbočini na zadku (Slika 1). Kako bi utvrdili prisutnost brezovog potkornjaka bjelikara na području Hrvatske, u ovom radu je napravljen pregled povijesnih zapisa (entomološke zbirke i literatura) i sastojina obične breze (B. pendula). Na terenu su sakupljeni uzorci (trupčići) na kojima je uočena prisutnost brezovog potkornjaka bjelikara te je napravljena laboratorijska analiza. Pregledom literature utvrđen je posljednji zabilježeni pronalazak brezovog potkornjaka bjelikara od prije više od 100 godina (1913. godina), a primjerci u entomološkim zbirkama potječu iz susjednih zemalja. Terenski pregled sastojina obične breze utvrdio je pet novih lokacija na kojima je vidljiva prisutnost brezovog potkornjaka bjelikara (Slika 3; Tablica 1). Gustoća populacije ove vrste u šumskim i urbanim područjima Hrvatske je niska, ali bez obzira na tu činjenicu brezov potkornjak bjelikar predstavlja važan dio entomofaune Hrvatske. Nastavak istraživanja trebao bi razjasniti povezanost brezovog potkornjaka bjelikara s patogenim gljivičnim bolestima i foretičkim grinjama s obzirom na moguće promjene na južnom rubu područja rasprostranjenja obične breze

DisProt 7.0 : a major update of the database of disordered proteins

Erratum: Nucleic Acids Res (2017) 45 (D1): D1123-D1124.The publishers would like to apologise for a mistake in the affiliation of one of the authors, Salvador Ventura. The correct affiliation is Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain. This has now been corrected online

Structural, Optical and Electrical Properties of Al+MoO3 and Au+MoO3 Thin Films Prepared by Magnetron Codeposition

Structural, optical and electrical properties of Al+MoO3 and Au+MoO3 thin films prepared by simultaneous magnetron sputtering deposition were investigated. The influence of MoO3 sputtering power on the Al and Au nanoparticle formation and spatial distribution was explored. We demonstrated the formation of spatially arranged Au nanoparticles in the MoO3 matrix, while Al incorporates in the MoO3 matrix without nanoparticle formation. The dependence of the Au nanoparticle size and arrangement on the MoO3 sputtering power was established. The Al-based films show a decrease of overall absorption with an Al content increase, while the Au-based films have the opposite trend. The transport properties of the investigated films also are completely different. The resistivity of the Al-based films increases with the Al content, while it decreases with the Au content increase. The reason is a different transport mechanism that occurs in the films due to their different structural properties. The choice of the incorporated material (Al or Au) and its volume percentage in the MoO3 matrix enables the design of materials with desirable optical and electrical characteristics for a variety of applications. © 2021 by the authors

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nuclear magnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics. Predictions have been expanded to provide new types of annotation on backbone rigidity, secondary structure preference and disordered binding regions. MobiDB 3.0 contains information for the complete UniProt protein set and synchronization has been improved by covering all UniParc sequences. An advanced search function allows the creation of a wide array of custom-made datasets for download and further analysis. A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility

Correction: Spatiotemporal distribution and speciation of silver nanoparticles in the healing wound.

Correction for 'Spatiotemporal distribution and speciation of silver nanoparticles in the healing wound' by Marco Roman et al., Analyst, 2020, 145, 6456–6469, DOI: 10.1039/D0AN00607F

DisProt 7.0: a major update of the database of disordered proteins

The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins

MobiDB: Intrinsically disordered proteins in 2021

The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.Fil: Piovesan, Damiano. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Escobedo, Nahuel Abel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Viczián, András. Università di Padova; ItaliaFil: Mičetić, Ivan. Università di Padova; ItaliaFil: Quaglia, Federica. Università di Padova; ItaliaFil: Paladin, Lisanna. Università di Padova; ItaliaFil: Ramasamy, Pathmanaban. Vrije Unviversiteit Brussel; Bélgica. University of Ghent; Bélgica. Interuniversity Institute of Bioinformatics in Brussels; BélgicaFil: Dosztányi, Zsuzsanna. Eötvös Loránd University; HungríaFil: Vranken, Wim F.. Vrije Unviversiteit Brussel; Bélgica. Interuniversity Institute of Bioinformatics in Brussels; BélgicaFil: Davey, Norman E.. The Institute Of Cancer Research; Reino UnidoFil: Parisi, Gustavo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Fuxreiter, Monika. Università di Padova; ItaliaFil: Tosatto, Silvio C. E.. Università di Padova; Itali

RepeatsDB in 2021: Improved data and extended classification for protein tandem repeat structures

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.Fil: Paladin, Lisanna. Università di Padova; ItaliaFil: Bevilacqua, Martina. Università di Padova; ItaliaFil: Errigo, Sara. Università di Padova; ItaliaFil: Piovesan, Damiano. Università di Padova; ItaliaFil: Mičetić, Ivan. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Fabre, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas; ArgentinaFil: López, José Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas; ArgentinaFil: Nilsson, Juliet Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas; ArgentinaFil: Ríos, Javier Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Lorenzano Menna, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Cabrera, Maia Diana Eliana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: González Buitrón, Martín. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Gonçalves Kulik, Mariane. Johannes Gutenberg Universitat Mainz; AlemaniaFil: Fernández Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Fornasari, Maria Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Parisi, Gustavo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Departamento de Ciencias Biológicas; ArgentinaFil: Hirsh, Layla. Pontificia Universidad Católica de Perú; PerúFil: Andrade Navarro, Miguel A.. Johannes Gutenberg Universitat Mainz; AlemaniaFil: Kajava, Andrey V. Centre National de la Recherche Scientifique; FranciaFil: Tosatto, Silvio C E. Università di Padova; Itali

Spatiotemporal distribution and speciation of silver nanoparticles in the healing wound

Funding: This research was supported by funds from the MIUR-FIRB project number RBFR08M6W8. Acknowledgments: ELGA LabWater is acknowledged for providing the PURELAB Option-Q and Ultra Analytic systems, which produced the ultra-pure water used for Ag determinations. Adam Douglas and Dhinesh Asogan are acknowledged for their technical support during LA-ICP-MS analysis at the University of Venice, and the authors gratefully acknowledge Bill Spence and Teledyne Cetac Technologies for the loan of the laser ablation instrumentation. Laura Molin and ISTM-CNR are acknowledged for MALDI-TOF-MS analysis. The synchrotron experiments were performed on beamline ID21 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France (proposal #CH4121).Peer reviewedPostprin

Tools and data services registry: a community effort to document bioinformatics resources

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools