Perspectives in science最新文献

Urinary tract infections (UTIs), which are among the most prevalent bacterial infections worldwide, are mainly attributed to uropathogenic Escherichia coli (UPEC). Because of frequent antibiotic treatment, antimicrobial resistance constitutes an increasing therapeutic problem. Antagonists of the mannose-specific bacterial lectin FimH, a key protein mediating the adhesion of UPEC to human bladder cells, would offer an alternative anti-adhesive treatment strategy. In general, FimH antagonists consist of a mannose moiety and a wide range of lipophilic aglycones. Modifications of the mannose core led to a distinct drop in affinity. A visual inspection of the crystal structure of FimH revealed a previously unexplored cavity surrounded by Ile13, Phe142 and Asp140, which could be reached by functional groups in the equatorial 2-position of the mannose. Here, we describe the synthesis of 2-C-branched mannosides and evaluation of their pharmacodynamic properties. ITC experiments with the selected antagonists revealed a drastic enthalpy loss for all 2-C-branched antagonists, which, however, is partially compensated by an entropy gain. This supports the hypothesis that the target cavity is too small to accommodate 2-C-substituents.

High-throughput methods to identify and quantify glycans in a given sample are rare. We have optimised a robotic platform for analysing biopharmaceuticals at each stage of the manufacturing process. In addition, it can be applied to basic research. The plate format makes it convenient for large sample sets; it is relatively cheap, robust and quantitative. However, the large datasets churned out by this platform require significant time to interpret. Consequently, informatics tool are required to help with this annotation. This article briefly describes our robotic platform and concentrates on a set of software tools for the interpretation of quantitative glycoprofiling data.

Cell surface heparan sulfates modulate many signalling pathways by binding growth factors and growth factor receptors. Expressed in a spatially and temporally regulated manner, these highly sulfated polysaccharides play important roles in all aspects of animal physiology. To understand heparan sulfate-protein binding, it is necessary to develop instrumental sequencing methods. Towards this end, we and others have demonstrated the effectiveness of activated electron dissociation (ExD) tandem mass spectrometry. The value in the ExD approach is that extremely rich tandem mass spectra are produced. The challenge is that bioinformatics methods are needed to convert the raw data into HS saccharide sequences. In this article we describe HS–SEQ, an algorithm developed for this purpose.

Protein–glycan interactions are ubiquitous in nature. Molecular description of complex formation and the underlying thermodynamics, however, are not well understood due to the lack of model systems. Bacteriophage tailspike proteins (TSP) possess binding sites for bacterial cell surfaces oligosaccharides. In this article we describe the analysis of TSP-oligosaccharide complexes. TSP provide large glycan interaction sites where affinity and specificity are guided by the protein surface solvation and the conformational space sampled by the respective glycan. Furthermore, we describe a computational approach to analyse the conformational space sampled by flexible glycans of bacterial origin, a prerequisite for a thorough understanding of TSP-oligosaccharide interactions.

The GLYcan Data Exchange (GLYDE) standard has been developed for the representation of the chemical structures of monosaccharides, glycans and glycoconjugates using a connection table formalism formatted in XML. This format allows structures, including those that do not exist in any database, to be unambiguously represented and shared by diverse computational tools. GLYDE implements a partonomy model based on human language along with rules that provide consistent structural representations, including a robust namespace for specifying monosaccharides. This approach facilitates the reuse of data processing software at the level of granularity that is most appropriate for extraction of the desired information. GLYDE-II has already been used as a key element of several glycoinformatics tools. The philosophical and technical underpinnings of GLYDE-II and recent implementation of its enhanced features are described.

Carbohydrates are the dominant biopolymer on earth and play important roles ranging from building material for plants to function in many biological systems. Glycans remain poorly studied due to a lack of synthetic tools. The goal of my laboratory has been to develop a general method for the automated assembly of glycans. The general protocols we developed resulted in the commercialisation of the Glyconeer 2.1™ synthesizer as well as the building blocks and all reagents. Oligosaccharides as long as 50-mers are now accessible within days. Rapid access to defined oligosaccharides has been the foundation to many applications including synthetic tools such as glycan microarrays, glycan nanoparticles and anti-glycan antibodies. The platform technology is helping to address real-life problems by the creation of new vaccines and diagnostics. After addressing mainly mammalian glycobiology earlier, material science and plant biology are benefitting increasingly from synthetic glycans.

Sulfated glycosaminoglycans (GAGs) are complex polysaccharides, which are covalently bound to protein cores to form proteoglycans. They are mostly located at the cell surface and in the extracellular matrix (ECM) where they regulate numerous biological processes. The aim of our work is (i) to identify and characterize protein–GAG interactions occurring at the cell surface and in the ECM, (ii) to study the assembly of multimolecular complexes formed at the cell surface via protein–heparan sulfate interactions, (iii) to determine the roles of these complexes in the ECM maturation and assembly, which are initiated in the pericellular matrix, and in pathological situations such as angiogenesis and host–pathogen interactions, (iv) to build, contextualize and analyze the corresponding protein–heparan sulfate interaction networks to identify molecular connections between the physio-pathological processes mentioned above and to select protein–GAG complexes specifically formed in a pathological situation and which might be therapeutic targets.

Examination of the chemical step catalysed by dihydrofolate reductase (DHFR) suggested preservation of an “ideal” transition state as the enzyme evolves from bacteria to human. This observation is enigmatic: since evolutionary pressure is most effective on enzymes’ second order rate constant (k_cat/K_M) and since the chemistry is not rate limiting on that kinetic parameter, why is the nature of the chemical step preserved? Studies addressing this question were presented in the 2015 Beilstein ESCEC Symposium and are summarized below.

Obwohl bislang kaum Untersuchungen zur optimalen zeitlichen Strukturierung von Unterricht vorliegen, verlängern einige Schulen in Deutschland zurzeit die Schulstundenlänge auf 60 (auch 65 oder 67,5 usw.) Minuten. Die vorliegende empirische Studie untersucht die Auswirkungen der Stundenverlängerung auf die Unterrichtsqualität im Physikunterricht der Sekundarstufe I. Dazu wurde der 60-Minuten-Unterricht von zwei Lehrkräften aufgezeichnet und ausgewertet und mit dem 45-Minuten-Unterricht derselben Lehrkräfte aus einer früheren Studie verglichen (n = 14 Videos). Die Analyse erfolgt unter dem Blickwinkel der Basismodelle nach Oser mit ergänzenden Sichtweisen aus Befragungen von Schülerinnen und Schülern sowie Lehrern und einem Expertenrating zur Unterrichtsqualität. Zentrales Ergebnis für die untersuchten Fälle ist, dass die längeren Unterrichtstunden eine höhere didaktische Vielfalt in Bezug auf die Lehrzielwahl aufweisen, und dass in den längeren Unterrichtsstunden mehr Lernprozesse abgeschlossen werden können. Jedoch bleibt das Maß an kognitiver Aktivität der Schülerinnen und Schüler gleich. Außerdem gibt es Hinweise auf eine zeitliche Ausdehnung der Wiederholungsphase bei den längeren Stunden. Zusammengefasst bieten die längeren Schulstunden das Potenzial für eine Qualitätsverbesserung.