56 research outputs found
Improving phylogeny reconstruction at the strain level using peptidome datasets
Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.This research was funded by Grant AGL2013-44039-R from the Spanish âPlan Estatal de I+D+Iâ, and by Grant EM2014/046 from the âPlan Galego de investigaciĂłn, innovaciĂłn e crecemento 2011-2015â. BS was recipient of a RamĂłn y Cajal postdoctoral contractfrom the Spanish Ministry of Economyand Competitiveness. This work was also partially funded by the [14VI05] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273).The research leading to these results has also received funding from the European Unionâs Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement nË 316265, BIOCAPS. This document reflects only the authorsâ views and the European Union is not liable for any use that may be made of the information contained herein. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
PP13, Maternal ABO Blood Groups and the Risk Assessment of Pregnancy Complications
Placental Protein 13 (PP13), an early biomarker of preeclampsia, is a placenta-specific galectin that binds beta-galactosides, building-blocks of ABO blood-group antigens, possibly affecting its bioavailability in blood.We studied PP13-binding to erythrocytes, maternal blood-group effect on serum PP13 and its performance as a predictor of preeclampsia and intrauterine growth restriction (IUGR). Datasets of maternal serum PP13 in Caucasian (nâ=â1078) and Hispanic (nâ=â242) women were analyzed according to blood groups. In vivo, in vitro and in silico PP13-binding to ABO blood-group antigens and erythrocytes were studied by PP13-immunostainings of placental tissue-microarrays, flow-cytometry of erythrocyte-bound PP13, and model-building of PP13--blood-group H antigen complex, respectively. Women with blood group AB had the lowest serum PP13 in the first trimester, while those with blood group B had the highest PP13 throughout pregnancy. In accordance, PP13-binding was the strongest to blood-group AB erythrocytes and weakest to blood-group B erythrocytes. PP13-staining of maternal and fetal erythrocytes was revealed, and a plausible molecular model of PP13 complexed with blood-group H antigen was built. Adjustment of PP13 MoMs to maternal ABO blood group improved the prediction accuracy of first trimester maternal serum PP13 MoMs for preeclampsia and IUGR.ABO blood group can alter PP13-bioavailability in blood, and it may also be a key determinant for other lectins' bioavailability in the circulation. The adjustment of PP13 MoMs to ABO blood group improves the predictive accuracy of this test
Bioinformatics and molecular modeling in glycobiology
The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and proteinâcarbohydrate interaction are reviewed
«La relation de limitation et dâexception dans le français dâaujourdâhui : exceptĂ©, sauf et hormis comme pivots dâune relation algĂ©brique »
Lâanalyse des emplois prĂ©positionnels et des emplois conjonctifs dâ âexceptĂ©â, de âsaufâ et dâ âhormisâ permet dâenvisager les trois prĂ©positions/conjonctions comme le pivot dâun binĂŽme, comme la plaque tournante dâune structure bipolaire. PlacĂ©es au milieu du binĂŽme, ces prĂ©positions sont forcĂ©es par leur sĂ©mantisme originaire dĂ»ment mĂ©taphorisĂ© de jouer le rĂŽle de marqueurs dâinconsĂ©quence systĂ©matique entre lâĂ©lĂ©ment se trouvant Ă leur gauche et celui qui se trouve Ă leur droite. Lâopposition qui surgit entre les deux Ă©lĂ©ments nâest donc pas une incompatibilitĂ© naturelle, intrinsĂšque, mais extrinsĂšque, induite. Dans la plupart des cas (emplois limitatifs), cette opposition prend la forme dâun rapport entre une « classe » et le « membre (soustrait) de la classe », ou bien entre un « tout » et une « partie » ; dans dâautres (emplois exceptifs), cette opposition se manifeste au contraire comme une attaque de front portĂ©e par un « tout » Ă un autre « tout ». De plus, lâinconsĂ©quence induite mise en place par la prĂ©position/conjonction paraĂźt, en principe, tout Ă fait insurmontable. Dans lâassertion « les Ă©cureuils vivent partout, sauf en Australie » (que lâon peut expliciter par « Les Ă©cureuils vivent partout, sauf [quâils ne vivent pas] en Australie »), la prĂ©position semble en effet capable dâimpliquer le prĂ©dicat principal avec signe inverti, et de bĂątir sur une telle implication une sorte de sous Ă©noncĂ© qui, Ă la rigueur, est totalement inconsĂ©quent avec celui qui le prĂ©cĂšde (si « les Ă©cureuils ne vivent pas en Australie », le fait quâils « vivent partout » est faux). NĂ©anmoins, lâanalyse montre quâalors que certaines de ces oppositions peuvent enfin ĂȘtre dĂ©passĂ©es, dâautres ne le peuvent pas. Câest, respectivement, le cas des relations limitatives et des relations exceptives. La relation limitative, impliquant le rapport « tout » - « partie », permet de rĂ©soudre le conflit dans les termes dâune somme algĂ©brique entre deux sous Ă©noncĂ©s pourvus de diffĂ©rent poids informatif et de signe contraire. Les valeurs numĂ©riques des termes de la somme Ă©tant dĂ©sĂ©quilibrĂ©es, le rĂ©sultat est toujours autre que zĂ©ro. La relation exceptive, au contraire, qui nâimplique pas le rapport « tout » - « partie », nâest pas capable de rĂ©soudre le conflit entre deux sous Ă©noncĂ©s pourvus du mĂȘme poids informatif et en mĂȘme temps de signe contraire : les valeurs numĂ©riques des termes de la somme Ă©tant symĂ©triques et Ă©gales, le rĂ©sultat sera toujours Ă©quivalent Ă zĂ©ro
The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics
The Chemistry Development Kit (CDK) is a freely available open- source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborator
The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics.
The Chemistry Development Kit (CDK) is a freely available open- source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborator
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