Perspectives in science最新文献

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2-C-Branched mannosides as a novel family of FimH antagonists—Synthesis and biological evaluation 2- c支链甘露糖作为一类新的FimH拮抗剂——合成及生物学评价
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.10.002
Wojciech Schönemann, Marcel Lindegger, Said Rabbani, Pascal Zihlmann, Oliver Schwardt, Beat Ernst
{"title":"2-C-Branched mannosides as a novel family of FimH antagonists—Synthesis and biological evaluation","authors":"Wojciech Schönemann,&nbsp;Marcel Lindegger,&nbsp;Said Rabbani,&nbsp;Pascal Zihlmann,&nbsp;Oliver Schwardt,&nbsp;Beat Ernst","doi":"10.1016/j.pisc.2016.10.002","DOIUrl":"10.1016/j.pisc.2016.10.002","url":null,"abstract":"<div><p>Urinary tract infections (UTIs), which are among the most prevalent bacterial infections worldwide, are mainly attributed to uropathogenic <em>Escherichia coli</em> (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-<em>C</em>-branched mannosides and evaluation of their pharmacodynamic properties. ITC experiments with the selected antagonists revealed a drastic enthalpy loss for all 2-<em>C</em>-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-<em>C</em>-substituents.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 53-61"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83288171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Bioinformatics applications to aid high-throughput glycan profiling 生物信息学应用,以帮助高通量聚糖分析☆
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.01.013
Ian Walsh, Roisin O’Flaherty, Pauline M. Rudd
{"title":"Bioinformatics applications to aid high-throughput glycan profiling","authors":"Ian Walsh,&nbsp;Roisin O’Flaherty,&nbsp;Pauline M. Rudd","doi":"10.1016/j.pisc.2016.01.013","DOIUrl":"10.1016/j.pisc.2016.01.013","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 31-39"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.01.013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88707299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Bioinformatics of glycosaminoglycans 糖胺聚糖的生物信息学
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.01.014
Han Hu , Yang Mao , Yu Huang , Cheng Lin , Joseph Zaia
{"title":"Bioinformatics of glycosaminoglycans","authors":"Han Hu ,&nbsp;Yang Mao ,&nbsp;Yu Huang ,&nbsp;Cheng Lin ,&nbsp;Joseph Zaia","doi":"10.1016/j.pisc.2016.01.014","DOIUrl":"10.1016/j.pisc.2016.01.014","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 40-44"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.01.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82697433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Complex carbohydrate recognition by proteins: Fundamental insights from bacteriophage cell adhesion systems 蛋白质对复杂碳水化合物的识别:来自噬菌体细胞粘附系统的基本见解
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.10.001
Nina K. Broeker , Dorothee Andres , Yu Kang , Ulrich Gohlke , Andreas Schmidt , Sonja Kunstmann , Mark Santer , Stefanie Barbirz
{"title":"Complex carbohydrate recognition by proteins: Fundamental insights from bacteriophage cell adhesion systems","authors":"Nina K. Broeker ,&nbsp;Dorothee Andres ,&nbsp;Yu Kang ,&nbsp;Ulrich Gohlke ,&nbsp;Andreas Schmidt ,&nbsp;Sonja Kunstmann ,&nbsp;Mark Santer ,&nbsp;Stefanie Barbirz","doi":"10.1016/j.pisc.2016.10.001","DOIUrl":"10.1016/j.pisc.2016.10.001","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 45-52"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73341851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
GLYDE-II: The GLYcan data exchange format GLYDE-II: GLYcan数据交换格式
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.05.013
Rene Ranzinger , Krys J. Kochut , John A. Miller , Matthew Eavenson , Thomas Lütteke , William S. York
{"title":"GLYDE-II: The GLYcan data exchange format","authors":"Rene Ranzinger ,&nbsp;Krys J. Kochut ,&nbsp;John A. Miller ,&nbsp;Matthew Eavenson ,&nbsp;Thomas Lütteke ,&nbsp;William S. York","doi":"10.1016/j.pisc.2016.05.013","DOIUrl":"10.1016/j.pisc.2016.05.013","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 24-30"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.05.013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35449611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Glycan arrays and other tools produced by automated glycan assembly 聚糖阵列和其他由自动聚糖组装产生的工具
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.06.085
Peter H. Seeberger
{"title":"Glycan arrays and other tools produced by automated glycan assembly","authors":"Peter H. Seeberger","doi":"10.1016/j.pisc.2016.06.085","DOIUrl":"10.1016/j.pisc.2016.06.085","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 11-17"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.06.085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83689333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Protein–glycosaminoglycan interaction networks: Focus on heparan sulfate 蛋白-糖胺聚糖相互作用网络:关注硫酸肝素☆
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.10.004
Sylvie Ricard-Blum
{"title":"Protein–glycosaminoglycan interaction networks: Focus on heparan sulfate","authors":"Sylvie Ricard-Blum","doi":"10.1016/j.pisc.2016.10.004","DOIUrl":"10.1016/j.pisc.2016.10.004","url":null,"abstract":"<div><p>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 <em>via</em> 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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 62-69"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.10.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80485211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
Unravelling glycan complexity—Prologue 揭开聚糖的复杂性——序言☆
Perspectives in science Pub Date : 2017-01-01 DOI: 10.1016/j.pisc.2016.10.003
Carsten Kettner, Martin G. Hicks
{"title":"Unravelling glycan complexity—Prologue","authors":"Carsten Kettner,&nbsp;Martin G. Hicks","doi":"10.1016/j.pisc.2016.10.003","DOIUrl":"10.1016/j.pisc.2016.10.003","url":null,"abstract":"","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"11 ","pages":"Pages 1-2"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.10.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76099614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The enigmatic conservation of enzyme dynamics in evolution 进化过程中酶动力学的神秘守恒
Perspectives in science Pub Date : 2016-12-01 DOI: 10.1016/j.pisc.2016.03.023
Amnon Kohen
{"title":"The enigmatic conservation of enzyme dynamics in evolution","authors":"Amnon Kohen","doi":"10.1016/j.pisc.2016.03.023","DOIUrl":"10.1016/j.pisc.2016.03.023","url":null,"abstract":"<div><p>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 (<em>k</em><sub>cat</sub>/<em>K</em><sub>M</sub>) 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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"9 ","pages":"Pages 60-66"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2016.03.023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75192280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Der Einfluss der Stundenlänge (45 vs. 60 Minuten) auf ausgewählte Aspekte der Unterrichtsqualität im Physikunterricht am Gymnasium 每小时(45到60分钟)对高校物理教学质量所选几个方面的影响:一次文职的调查,也有两个教师
Perspectives in science Pub Date : 2016-12-01 DOI: 10.1016/j.pisc.2015.12.009
R. Wackermann, J. Hater
{"title":"Der Einfluss der Stundenlänge (45 vs. 60 Minuten) auf ausgewählte Aspekte der Unterrichtsqualität im Physikunterricht am Gymnasium","authors":"R. Wackermann,&nbsp;J. Hater","doi":"10.1016/j.pisc.2015.12.009","DOIUrl":"10.1016/j.pisc.2015.12.009","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":92112,"journal":{"name":"Perspectives in science","volume":"10 ","pages":"Pages 1-12"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.pisc.2015.12.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85435247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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