Global hydrodynamic analysis of the molecular flexibility of galactomannans

In the past, intrinsic viscosity and sedimentation velocity analyses have been used separately to assess the conformation and flexibility of guar and locust bean gum galactomannans based on worm-like chain and semi-flexible coil models. Publication of a new global method combining data sets of both intrinsic viscosity and sedimentation coefficient with molecular weight, and minimising a target (error) function now permits a more robust analysis. Using this approach, values for the persistence length of (10 ± 2) nm for guar and (7 ± 1) nm for locust bean gum are returned if the mass per unit length ML is floated as a variable. Using a fixed mass per unit length based on the known compositional data of each galactomannan yields a similar value for Lp in both cases, (8 ± 1) nm for guar and (9 ± 1) nm for locust bean gum, with combined set of data yielding (9 ± 1) nm: within experimental error the flexibilities of both galactomannans are very similar. © 2007 Elsevier Ltd. All rights reserved

Rheology of Biopolymer Solutions and Gels

Rheological techniques and methods have been employed for many decades in the characterization of polymers. Originally developed and used on synthetic polymers, rheology has then found much interest in the field of natural (bio) polymers. This review concentrates on introducing the fundamentals of rheology and on discussing the rheological aspects and properties of the two major classes of biopolymers: polysaccharides and proteins. An overview of both their solution properties (dilute to semi-dilute) and gel properties is described

Molecular flexibility of citrus pectins by combined sedimentation and viscosity analysis

The flexibility/rigidity of pectins plays an important part in their structure-function relationship and therefore on their commercial applications in the food and biomedical industries. Earlier studies based on sedimentation analysis in the ultracentrifuge have focused on molecular weight distributions and qualitative and semi-quantitative descriptions based on power law and Wales-van Holde treatments of conformation in terms of "extended" conformations [Harding, S. E., Berth, G., Ball, A., Mitchell, J.R., & Garcìa de la Torre, J. (1991). The molecular weight distribution and conformation of citrus pectins in solution studied by hydrodynamics. Carbohydrate Polymers, 168, 1-15; Morris, G. A., Foster, T. J., & Harding, S.E. (2000). The effect of degree of esterification on the hydrodynamic properties of citrus pectin. Food Hydrocolloids, 14, 227-235]. In the present study, four pectins of low degree of esterification 17-27% and one of high degree of esterification (70%) were characterised in aqueous solution (0.1 M NaCl) in terms of intrinsic viscosity [η], sedimentation coefficient (s°20,w) and weight average molar mass (Mw). Solution conformation/flexibility was estimated qualitatively using the conformation zoning method [Pavlov, G.M., Rowe, A.J., & Harding, S.E. (1997). Conformation zoning of large molecules using the analytical ultracentrifuge. Trends in Analytical Chemistry, 16, 401-405] and quantitatively (persistence length Lp) using the traditional Bohdanecky and Yamakawa-Fujii relations combined together by minimisation of a target function. Sedimentation conformation zoning showed an extended coil (Type C) conformation and persistence lengths all within the range Lp=10-13 nm (for a fixed mass per unit length)

Intragastric structuring of anionic polysaccharide kappa-carrageenan filled gels under physiological in vitro digestion conditions

In the present work, sodium alginate (SA), low methoxyl pectin (PEC) and κ-carrageenan (κ-CAR) were evaluated for their intragastric structuring ability by means of light microscopy and dynamic oscillatory rheology. SA and PEC solutions, their Ca2+ complexed gel analogues as well as their binary blends with ionically or thermally set sheared κ-CAR gels, were subjected to in vitro orogastric conditions. SA and PEC – Ca2+ complexed sheared gels exerted the highest vulnerability to digestive fluid exposure due to the dialysis of egg-box dimer structures via proton-calcium exchange. Incorporation of SA and PEC systems to κ-CAR gels prevented the loss of mechanical strength of the gastric gels due to the ability of κ-CAR to undergo spontaneous gelation in the presence of Na+ and K+ ions. Binary blends of SA and PEC – Ca2+ complexed sheared gels with κ-CAR-Ca2+ gels exerted a significantly lower mechanical strength loss sensitivity against pH and counterion composition of the gastric fluids

Spatial mapping of flow-induced molecular alignment in a noncrystalline biopolymer fluid using double quantum filtered (DQF) 23Na MRI

Flow-induced molecular alignment was observed experimentally in a non-liquid- crystalline bioplymeric fluid during developed tubular flow. The fluid was comprised of rigid rods of the polysaccharide xanthan and exhibited shear-thinning behavior. Without a requirement for optical transparency or the need for an added tracer, 23Na magic angle (MA) double quantum filtered (DQF) magnetic resonance imaging (MRI) enabled the mapping of the anisotropic molecular arrangement under flow conditions. A regional net molecular alignment was found in areas of high shear values in the vicinity of the tube wall. Furthermore, the xanthan molecules resumed random orientations after the cessation of flow. The observed flow-induced molecular alignment was correlated with the rheological properties of the fluid. The work demonstrates the ability of 23Na MA DQF magnetic resonance to provide a valuable molecular-mechanical link

Polysaccharide structures and interactions in a lithium chloride/urea/water solvent

The molten salt hydrate, lithium chloride (LiCl)/urea/water has previously been shown to swell cellulose, but there has so far been no work done to explore its effect on other polysaccharides. In this paper we have investigated the solvent effects of LiCl/urea/water on four natural polysaccharides. Fenugreek gum and xyloglucan, which are both highly branched, were found to increase in viscosity in LiCl/urea/water relative to water, possibly due to the breakage of all intra-molecular associations whereas the viscosity of konjac glucomannan which is predominantly unbranched did not change. Locust bean gum (LBG) had a lower viscosity in LiCl/urea/water compared to water due to the disruption of aggregates. Confocal microscopy showed that fenugreek gum and LBG are able to bind to cellulose in water, however, the conformational change of fenugreek gum in these solvent conditions inhibited it from binding to cellulose in LiCl/urea/water whereas conformational change allowed xyloglucan to bind to cellulose in LiCl/urea/water whilst it was unable to bind in water. Konjac glucomannan did not bind to cellulose in either solvent system. These results provide new insights into the impact of polysaccharide fine structure on conformational change in different solvent environments

Ultracentrifuge methods for the analysis of polysaccharides, glycoconjugates, and lignins

Although like proteins, polysaccharides are synthesized by enzymes, unlike proteins there is no template. This means that they are polydisperse, do not generally have compact folded structures, and are often very large with greater nonideality behavior in solution. This chapter considers the relevant analytical ultracentrifuge methodology available for characterizing these and related carbohydrate-based systems and information this methodology supplies, in terms of sizes, shapes, and interactions using a comprehensive range of examples, including glycoconjugates and lignins. The relevance and potential of recent software developments such as SEDFIT-MSTAR, the Extended Fujita algorithm, and HYDFIT are considered

How to Integrate and Share Distributed Biobank Data by Using an IT-Based Semantic Approach

Semantische Methoden zur Vereinfachung von Datenintegration und Datenaustausch in der Biomedizin wurden in zahlreichen Studien behandelt und vorgestellt. Solche Methoden wurden bis jetzt allerdings nur begrenzt im Bereich der Biobanken angewandt. Durch die steigende Menge an Daten und wissenschaftlichen Kooperationen in diesem Bereich gewann die Integration und Harmonisierung von Forschungsdaten aus Biobanken auf semantischer sowie auf technischer Ebene zunehmend an Bedeutung, was sich in jüngsten Forschungsaktivitäten wiederspiegelt. Verschiedene Ontologien und Repräsentationsstandards wurden mit dem Ziel entwickelt, Biobankinhalte über gemeinsamn IT-Plattformen in harmonisierter Form zu teilen. Der Austausch und die Harmonisierung von Biobankinhalten in gemeinsamen IT-Plattformen verbessern die Auffindbarkeit wichtiger, forschungsrelevanter Proben und ermöglichen Betreibern einer Biobank oftmals die Teilnahme an transnationalen Forschungsprojekten. Diese Arbeit beschäftigt sich mit computergestützten, semantischen Methoden für den Vergleich, die Integration und den Austausch von Biobankdaten, welche in heterogenen Informationssystemen und Datenbanken gespeichert sind. Die erste Forschungsfrage befasst sich mit der Problematik, wie Probensammlungen und dazugehörige Datenquellen einer verteilten, krankenhausweiten Biobank in einer gemeinsamen Forschungsinfrastruktur identifiziert, vereinheitlicht und geteilt werden können. In diesem Kontext wurde die Anwendbarkeit eines internationalen Standardmodell sowie eines IT-gestützten Verfahrens zur Analyse von Krankenhausinfrastrukturen untersucht. Basierend auf den Ergebnissen dieser Untersuchung wurde ein erweitertes Datenmodell sowie ein krankenhausweiter elektronischer Katalog zur vereinheitlichten Abbildung und technischen Integration von Probensammlungen und Daten einer verteilten Biobankinfrastruktur konzeptioniert und in einer Studie vorgestellt. Die zweite Forschungsfrage befasst sich mit der Anwendbarkeit IT-gestützter, textbasierter Analyse- und Suchverfahren zur Identifikation und Evaluierung geeigneter (bio-) medizinischer Ontologien im Bereich von Biobanken. Diese wurde anhand eines ersten IT-gestützten Prototyps zur Evaluierung (bio-)medizinischer Ontologien basierend auf Kompetenzfragen gezeigt und in einer weiteren Publikation vorgestellt. Im Rahmen einer dritten Studie wurde die Möglichkeit einer IT-gestützten Annotation von Freitextdaten in Biobankplattformen zur verbesserten Auffindbarkeit und Vergleichbarkeit von Freitextinhalten in Biobanksystemen untersucht. Die technische Umsetzbarkeit wurde anhand eines semi-automatisierten Empfehlungssystems gezeigt, welches auf Basis textbasierter Suchalgorithmen Freitextdiagnosen mit semantischen Informationen aus (bio-) medizinischen Ontologien in einer graph-basierten Datenbankstruktur verknüpft und dem Benutzer vorschlägt. Die vierte Studie befasst sich mit semantischen und technischen Herausforderungen und IT-gestützten Möglichkeiten für die Harmonisierung und die technische Integration von Daten aus regionalen Biobanken in gemeinsamen nationalen und europäischen Forschungsinfrastrukturen. In dieser Arbeit wurden bekannte Ansätze zur Datenharmonisierung angewandt sowie Grundsätze für den elektronischen Austausch von Biobankdaten aus verschiedenen Katalogen erarbeitet.Various studies on using semantic techniques have been conducted to facilitate data integration and electronic data interchange in biomedicine. However, there have been limited applications to biobanks so far. Due to the growing amount of data and research collaboration in this area, there is an increasing demand for data integration and harmonization, both on semantic and technical level, which is reflected by ongoing research activities. Ontologies and standards were implemented for the purpose of sharing and harmonizing biobank data in common IT-platforms enabling biobank administrators to make their biobank available to the public, thereby improving the availability of relevant samples and transnational collaboration in research. This thesis investigates computer-assisted, semantic approaches for comparing, integrating and sharing biobank data across heterogeneous IT-systems and databases and provides different IT-based solutions which are described in the studies presented below in this thesis. The first research question was on how to identify, standardize and share biobank data resources from a distributed, hospital-wide biobank in a common research infrastructure. For this, an existing international standard data model and IT-healthcare analysis method was applied to this context. Based on these methods, we implemented an extended standard data model which was used in a common hospital-wide biobank registry for sharing sample collections stored in different databases and information systems. Secondly, we explored the applicability of natural language processing and query expansion techniques for the evaluation of (bio-) medical ontologies for the biobanking domain. This resulted in a semi-automated evaluation approach for the evaluation of (bio-) medical ontologies based on competency questions. A third study explores the applicability of standard medical terminology concepts to annotate free-text data within biobank platforms. We implemented a prototype of a graph-based, semi-automated concept recommendation. The fourth study tackles the challenges of the harmonization and electronic data interchange of data from regional biobanks in common national and European research infrastructures. In this thesis, we demonstrate the transferability of semantic data harmonization approaches in the field of bioinformatics to the biobanking domain. Furthermore, we are confident that the approaches demonstrated in this thesis can be reused in biobanking and other medical research fields.Arbeit an der Bibliothek noch nicht eingelangt - Daten nicht geprüftAbweichender Titel laut Übersetzung der Verfasserin/des VerfassersInnsbruck, Univ., Diss., 2017(VLID)220897

Global conformation analysis of irradiated xyloglucans

Xyloglucan isolated and purified from tamarind seed was subjected to various degrees of γ-irradiation treatments, from 10 to 70 kGy, monitored for radiation damage and then studied using a new combined hydrodynamic approach with regards to conformation and flexibility. Radiation products were analysed with regard to molecular weight (weight average) Mw from size exclusion chromatography coupled to multi-angle laser light scattering (SEC-MALLs), intrinsic viscosity [η] and sedimentation coefficient so20,w. Sedimentation coefficient distributions and elution profiles from SEC-MALLs confirmed the unimodal nature of the molecular weight distribution for each sample in solution. The chain flexibility was then investigated in terms of the persistence length, Lp of the equivalent worm-like chain model. The traditional Bushin-Bohdanecky (intrinsic viscosity) and Yamakawa-Fujii (sedimentation coefficient) relations were used separately then combined together by minimisation of a target function according to a recently published procedure [Ortega, A., & García de la Torre, J. (2007). Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility. Biomacromolecules, 8, 2464-2475 [see also Ortega, A. Metodologías computacionales para propiedades en disolución de macromoléculas rígidas y flexibles. Ph.D. Dissertation, Universidad de Murcia, 2005]] and yielded an estimate for Lp in the range 4-9 nm using floated and fixed mass per unit length analysis protocols and "point" global analysis: irradiated xyloglucans behave as flexible structures in common with pressure/heat treated materials. © 2008 Elsevier Ltd. All rights reserved