Sollen wir Bibliothekare jetzt alle Informatiker werden? : Forschungsdatenmanagement, Datenerhaltung und -pflege als neue Aufgabenfelder

Immer mehr Bibliotheken übernehmen Aufgaben im Bereich der Datenerhaltung und -pflege. Informatiker/innen tragen im Öffentlichen Dienst oft die Bezeichnung »Angestellte/r in der Datenverwaltung«, obwohl die Verwaltung gespeicherter Daten schon lange keine Aufgabe mehr nur für Informatiker/innen darstellt. Gleichzeitig geht die bibliothekarische Arbeit über die klassische Literaturversorgung hinaus und umfasst zunehmend mehr und mehr technische Bereiche. Ein hochaktuelles Tätigkeitsfeld für wissenschaftliche Bibliotheken stellt das Forschungsdatenmanagement dar. Was verbirgt sich dahinter und welche Anforderungen ergeben sich daraus für das bibliothekarische Berufsbild? Sollen wir jetzt alle Informatiker/ innen werden

Datenmanagementpläne leicht gemacht: TUB-DMP, das Web-Tool der TU Berlin für Datenmanagementpläne

Das Web-Tool TUB-DMP ist ein weiterer Baustein in der Forschungsdaten-Infrastruktur der Technischen Universität Berlin, die vom „Servicezentrum Forschungsdaten und -publikationen“ (SZF) betrieben wird. TUB-DMP ergänzt das Repositorium für Forschungsdaten und Publikationen „Deposit-Once“, das die langfristige Verfügbarkeit, Verifizierung, Zitierbarkeit und Nachnutzbarkeit der Forschungsergebnisse gewährleistet. Forschungsdatenmanagement und ForschungsdatenInfrastruktur der TU Berlin sind nach den FAIR Data Principles (Findable, Accessible, Interoperable, Re-usable) ausgerichtet. Dieser Maßgabe entsprechend wurde auch TUB-DMP entwickelt, um den Wissenschaftlerinnen und Wissenschaftlern der TU Berlin ein Dokumentationswerkzeug an die Hand zu geben, das ein FAIRes Management ihrer Forschungsdaten ermöglicht. TUB-DMP wurde gemeinsam mit Pilotpartnern aus der TU Berlin entwickelt. Die erste Version wurde im September 2015 in Betrieb genommen, Version 2 mit einer Reihe von Erweiterungen im Dezember 2017.The TUB-DMP Web tool is a further component in the research data infrastructure of the Technische Universität Berlin (TU Berlin), which is operated by the Service Center for Research Data and Publications (SZF). TUB-DMP complements “DepositOnce”, the repository for research data and publications, which guarantees the long-term availability, verification, citability and re-usability of research results. The management of research data and the research data infrastructure at TU Berlin are aligned with the FAIR data principles (Findable, Accessible, Interoperable, Re-usable). TUB-DMP was developed according to these requirements in order to provide scientists with a documentation tool that enables the FAIR data management of their research data. TUB-DMP was developed in cooperation with pilot partners from TU Berlin. The first version went live in September 2015, the extended second version was released in December 201

Features of “All LNA” Duplexes Showing a New Type of Nucleic Acid Geometry

“Locked nucleic acids” (LNAs) belong to the backbone-modified nucleic acid family. The 2′-O,4′-C-methylene-β-D-ribofuranose nucleotides are used for single or multiple substitutions in RNA molecules and thereby introduce enhanced bio- and thermostability. This renders LNAs powerful tools for diagnostic and therapeutic applications. RNA molecules maintain the overall canonical A-type conformation upon substitution of single or multiple residues/nucleotides by LNA monomers. The structures of “all” LNA homoduplexes, however, exhibit significant differences in their overall geometry, in particular a decreased twist, roll and propeller twist. This results in a widening of the major groove, a decrease in helical winding, and an enlarged helical pitch. Therefore, the LNA duplex structure can no longer be described as a canonical A-type RNA geometry but can rather be brought into proximity to other backbone-modified nucleic acids, like glycol nucleic acids or peptide nucleic acids. LNA-modified nucleic acids provide thus structural and functional features that may be successfully exploited for future application in biotechnology and drug discovery

Cloning, sequencing, and overexpression of gene 16 of salmonella bacteriophage P22

Umlauf B, Dreiseikelmann B. Cloning, sequencing, and overexpression of gene 16 of salmonella bacteriophage P22. Virology. 1992;188(2):495-501.It has been suggested that gene product 16 of bacteriophage P22 forms a pore for DNA transfer and/or that it functions as a pilot protein guiding the DNA across the membrane. We have cloned gene 16 and determined the nucleotide sequence. Within the sequenced region there is an open reading frame that could encode a protein of 609 amino acids having a molecular weight of 64,366. The hydropathic plot of this protein does not reveal putative membrane-spanning regions as expected for a protein forming a membrane pore. Overproduction of gene product 16 in Escherichia coli was successful only in a mutant in which the La protease was inactivated. Gene 16 mutants of phage P22 were not able to infect recBCD mutants of Salmonella typhimurium nor was protein 16, synthesized in E. colifrom a plasmid, able to substitute for the pilot protein of phage T4. It seems that gene product 16 is not a pilot protein in the meaning of binding to the ends of linear DNA, thus protecting it from degradation by nucleases

An amphiphilic region in the cytoplasmic domain of KdpD is recognized by the signal recognition particle and targeted to the Escherichia coli membrane

The sensor protein KdpD of Escherichia coli is composed of a large N-terminal hydrophilic region (aa 1–400), four transmembrane regions (aa 401–498) and a large hydrophilic region (aa 499–894) at the C-terminus. KdpD requires the signal recognition particle (SRP) for its targeting to the membrane. Deletions within KdpD show that the first 50 residues are required for SRP-driven membrane insertion. A fusion protein of the green fluorescent protein (GFP) with KdpD is found localized at the membrane only when SRP is present. The membrane targeting of GFP was not observed when the first 50 KdpD residues were deleted. A truncated mutant of KdpD containing only the first 25 amino acids fused to GFP lost its ability to specifically interact with SRP, whereas a specific interaction between SRP and the first 48 amino acids of KdpD fused to GFP was confirmed by pull-down experiments. Conclusively, a small amphiphilic region of 27 residues within the amino-terminal domain of KdpD (aa 22–48) is recognized by SRP and targets the protein to the membrane. This shows that membrane proteins with a large N-terminal region in the cytoplasm can be membrane-targeted early on to allow co-translational membrane insertion of their distant transmembrane regions

The crystal structure of an ‘All Locked’ nucleic acid duplex

‘Locked nucleic acids’ (LNAs) are known to introduce enhanced bio- and thermostability into natural nucleic acids rendering them powerful tools for diagnostic and therapeutic applications. We present the 1.9 Å X-ray structure of an ‘all LNA’ duplex containing exclusively modified β-d-2′-O-4′C-methylene ribofuranose nucleotides. The helix illustrates a new type of nucleic acid geometry that contributes to the understanding of the enhanced thermostability of LNA duplexes. A notable decrease of several local and overall helical parameters like twist, roll and propeller twist influence the structure of the LNA helix and result in a widening of the major groove, a decrease in helical winding and an enlarged helical pitch. A detailed structural comparison to the previously solved RNA crystal structure with the corresponding base pair sequence underlines the differences in conformation. The surrounding water network of the RNA and the LNA helix shows a similar hydration pattern

PAAR-repeat proteins sharpen and diversify the Type VI secretion system spike

The bacterial type VI secretion system (T6SS) is a large multi-component, dynamic macromolecular machine that plays an important role in the ecology of many Gram negative bacteria. T6SS is responsible for translocation of a wide range of toxic effector molecules allowing predatory cells to kill both prokaryotic as well as eukaryotic prey cells1-5. The T6SS organelle is functionally analogous to contractile tails of bacteriophages and is thought to attack cells by initially penetrating them with a trimeric protein complex called the VgrG spike6,7. Neither the exact protein composition of the T6SS organelle nor the mechanisms of effector selection and delivery are known. Here we report that proteins from the PAAR (Proline-Alanine-Alanine-aRginine) repeat superfamily form a sharp conical extension on the VgrG spike, which is further involved in attaching effector domains to the spike. The crystal structures of two PAAR-repeat proteins bound to VgrG-like partners show that these proteins function to sharpen the tip of the VgrG spike. We demonstrate that PAAR proteins are essential for T6SS- mediated secretion and target cell killing by Vibrio cholerae and Acinetobacter baylyi. Our results suggest a new model of the T6SS organelle in which the VgrG-PAAR spike complex is decorated with multiple effectors that are delivered simultaneously into target cells in a single contraction-driven translocation event

Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action

Sialic acids are a family of related sugars that play essential roles in many biological events intimately linked to cellular recognition in both health and disease. Sialidases are therefore orchestrators of cellular biology and important therapeutic targets for viral infection. Here, we sought to define if uncharacterized sialidases would provide distinct paradigms in sialic acid biochemistry. We show that a recently discovered sialidase family, whose first member EnvSia156 was isolated from hot spring metagenomes, defines an unusual structural fold and active centre constellation, not previously described in sialidases. Consistent with an inverting mechanism, EnvSia156 reveals a His/Asp active center in which the His acts as a Bronsted acid and Asp as a Bronsted base in a single-displacement mechanism. A pre-dominantly hydrophobic aglycone site facilitates accommodation of a variety of 2-linked sialosides; a versatility that offers the potential for glycan hydrolysis across a range of biological and technological platforms

A Novel Extracytoplasmic Function (ECF) Sigma Factor Regulates Virulence in Pseudomonas aeruginosa

Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS systems sense signals from outside the cell and transmit them into the cytoplasm. They generally consist of a TonB-dependent outer membrane receptor, a sigma factor regulator (or anti-sigma factor) in the cytoplasmic membrane, and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa CSS systems are involved in the regulation of iron uptake, we have identified a novel system involved in the regulation of virulence. This CSS system, which has been designated PUMA3, has a number of unusual characteristics. The most obvious difference is the receptor component which is considerably smaller than that of other CSS outer membrane receptors and lacks a β-barrel domain. Homology modeling of PA0674 shows that this receptor is predicted to be a bilobal protein, with an N-terminal domain that resembles the N-terminal periplasmic signaling domain of CSS receptors, and a C-terminal domain that resembles the periplasmic C-terminal domains of the TolA/TonB proteins. Furthermore, the sigma factor regulator both inhibits the function of the ECF sigma factor and is required for its activity. By microarray analysis we show that PUMA3 regulates the expression of a number of genes encoding potential virulence factors, including a two-partner secretion (TPS) system. Using zebrafish (Danio rerio) embryos as a host we have demonstrated that the P. aeruginosa PUMA3-induced strain is more virulent than the wild-type. PUMA3 represents the first CSS system dedicated to the transcriptional activation of virulence functions in a human pathogen