Search

The application of angle-resolved fluorescence depolarization techniques to the simultaneous determination of the directions of the transition moments and orientational order of dye molecules incorporated into uniaxially stretched polymer films is discussed and illustrated. The directions of the transition moments of pyranine molecules are determined in a general way, on exciting the molecules in two distinct electronic transitions and monitoring the fluorescence emission under the same conditions. This assumes that the fluorescence emission occurs via the same transition moment for every excited absorption band. Experiments on perylene molecules show that the directions of the transition moments can also be determined from measurements utilizing a single electronic absorption band. In this case the orientational distribution of the molecules is assumed to have the form given by the maximum entropy method. Finally, it is shown the directions of the transition moments of DPH molecules in unstretched polymer films can be determined with this technique. It appears that these molecules are oriented to a very small, yet measurable, extent in unstretched films. [ABSTRACT FROM AUTHOR]

Background: Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Information File format (PDBx/mmCIF) is still not widespread. Perhaps one of the reasons is the availability of easy to use tools that only support the legacy format, but also the inherent difficulties of processing mmCIF files correctly, given the number of edge cases that make efficient parsing problematic. Nevertheless, to fully exploit macromolecular structure data and their associated annotations such as multiscale structures from integrative/hybrid methods or large macromolecular complexes determined using traditional methods, it is necessary to fully adopt the new format as soon as possible., Results: To this end, we developed PDBeCIF, an open-source Python project for manipulating mmCIF and CIF files. It is part of the official list of mmCIF parsers recorded by the wwPDB and is heavily employed in the processes of the Protein Data Bank in Europe. The package is freely available both from the PyPI repository ( http://pypi.org/project/pdbecif ) and from GitHub ( https://github.com/pdbeurope/pdbecif ) along with rich documentation and many ready-to-use examples., Conclusions: PDBeCIF is an efficient and lightweight Python 2.6+/3+ package with no external dependencies. It can be readily integrated with 3rd party libraries as well as adopted for broad scientific analyses., (© 2021. The Author(s).)

The aim of this study is to assess the relationship between pre- and perinatal factors and ADHD in a sample of scholars exploring differences between ADHD presentations and spectrum of severity. A total of 6720 scholars (aged 3-4 and 10-11) participated in a double-phase epidemiologic cross-sectional study (Epidemiological Study of Neurodevelopmental Disorders, EPINED), and a sample of 646 scholars (ADHD risk, ASD risk and controls without risk) were individually assessed in the second phase of the study. The ADHD diagnosis, based on DSM-5 criteria, was performed with the Kiddie-Schedule for Affective Disorders & Schizophrenia, Present & Lifetime Version. Associations for the different ADHD presentations between prenatal, perinatal and postnatal factors and ADHD (n = 168), subclinical ADHD (n = 88) and non-ADHD (n = 310) were analysed. Logistic regression models showed that gestational diabetes (p = 0.012), instrumental delivery (p = 0.011), family history of psychopathology (p = 0.033) and maternal ADHD phenotype (p = 0.023) were associated with ADHD. These factors were related to the hyperactive-impulsive and combined presentations, but they were not related to the inattentive presentation. Maternal weight gain was associated with subclinical ADHD. In conclusion, metabolic disorder in the pregnancy, difficulties in childbirth and specific family phenotype were related to ADHD, specifically with hyperactive-impulsive presentation, but not in subclinical ADHD.

Database Url: https://www.wwpdb.org/.

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments., (Published by Elsevier Ltd.)

The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination of macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science community to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.

The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration--it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.

We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html .

Under local mate competition, sex ratio theory predicts that increasing numbers of ovipositing females (foundresses) on a site should lead to higher proportions of males in their broods. Fig pollinators have confirmed this prediction. It is also predicted that with decreasing clutch size, solitary foundresses should produce increasing proportions of sons. We show this to be true. Further, when several females compete, brood size decreases. As a result, the proportion of males increases, and this could provide a mechanistic explanation of sex ratio response to numbers of colonizing females. Therefore, sex ratio data on fig wasps need to be reassessed to determine whether females 'count' other foundresses, as is generally accepted, or whether they simply 'count' the number of eggs that they lay.

Application of 10 successive daily heat shocks reduced the growth of control tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) plants by about 15%; for Phsp 70-ipt transformed plants this is about 48%. The shoot diameter of these ipt-transformed plants increased by about 75%. In addition, in heat shock treated ipt-plants (IPT-HS) the upper lateral buds grew out due to a reduction of apical dominance. The older leaves of IPT-HS plants had a higher chlorophyll content. In spite of the observed effects due to a higher endogenous cytokinin content in the IPT-HS plants, no significant changes were observed on the plasma membrane fatty acid composition, nor on its fluidity as determined from the steady-state fluorescence anisotropy of DPH. Only a minor change in the plasma membrane free sterol composition was found as evidenced by a 20% decrease in the stigmasterol to sitosterol ratio in IPT-HS, indicative for a possible anti-senescence effect of enhanced endogenous cytokinins, but without significant effects on the plasma membrane function.