Assessment of PEG on Polymeric Particles Surface, a Key Step in Drug Carrier Translation

Injectable drug nanocarriers have greatly benefited in their clinical development from the addition of a superficial hydrophilic corona to improve their cargo pharmacokinetics. The most studied and used polymer for this purpose is poly(ethylene glycol), PEG. However, in spite of its wide use for over two decades now, there is no general consensus on the optimum PEG chain coverage-density and size required to escape from the mononuclear phagocyte system and to extend the circulation time. Moreover, cellular uptake and active targeting may have conflicting requirements in terms of surface properties of the nanocarriers which complicates even more the optimization process. These persistent issues can be largely attributed to the lack of straightforward characterization techniques to assess the coverage-density, the conformation or the thickness of a PEG layer grafted or adsorbed on a particulate drug carrier and is certainly one of the main reasons why so few clinical applications involving PEG coated particle-based drug delivery systems are under clinical trial so far. The objective of this review is to provide the reader with a brief description of the most relevant techniques used to assess qualitatively or quantitatively PEG chain coverage-density, conformation and layer thickness on polymeric nanoparticles. Emphasis has been made on polymeric particle (solid core) either made of copolymers containing PEG chains or modified after particle formation. Advantages and limitations of each technique are presented as well as methods to calculate PEG coverage-density and to investigate PEG chains conformation on the NP surface.

Quantitative proteomics methods for the analysis of histone post-translational modifications

Les histones sont des protéines nucléaires hautement conservées chez les cellules des eucaryotes. Elles permettent d’organiser et de compacter l’ADN sous la forme de nucléosomes, ceux-ci representant les sous unités de base de la chromatine. Les histones peuvent être modifiées par de nombreuses modifications post-traductionnelles (PTMs) telles que l’acétylation, la méthylation et la phosphorylation. Ces modifications jouent un rôle essentiel dans la réplication de l’ADN, la transcription et l’assemblage de la chromatine. L’abondance de ces modifications peut varier de facon significative lors du developpement des maladies incluant plusieurs types de cancer. Par exemple, la perte totale de la triméthylation sur H4K20 ainsi que l’acétylation sur H4K16 sont des marqueurs tumoraux spécifiques a certains types de cancer chez l’humain. Par conséquent, l’étude de ces modifications et des événements determinant la dynamique des leurs changements d’abondance sont des atouts importants pour mieux comprendre les fonctions cellulaires et moléculaires lors du développement de la maladie. De manière générale, les modifications des histones sont étudiées par des approches biochimiques telles que les immuno-buvardage de type Western ou les méthodes d’immunoprécipitation de la chromatine (ChIP). Cependant, ces approches présentent plusieurs inconvénients telles que le manque de spécificité ou la disponibilité des anticorps, leur coût ou encore la difficulté de les produire et de les valider. Au cours des dernières décennies, la spectrométrie de masse (MS) s’est avérée être une méthode performante pour la caractérisation et la quantification des modifications d’histones. La MS offre de nombreux avantages par rapport aux techniques traditionnelles. Entre autre, elle permet d’effectuer des analyses reproductibles, spécifiques et facilite l’etude d’un large spectre de PTMs en une seule analyse. Dans cette thèse, nous présenterons le développement et l’application de nouveaux outils analytiques pour l’identification et à la quantification des PTMs modifiant les histones. Dans un premier temps, une méthode a été développée pour mesurer les changements d’acétylation spécifiques à certains sites des histones. Cette méthode combine l’analyse des histones intactes et les méthodes de séquençage peptidique afin de déterminer les changements d’acétylation suite à la réaction in vitro par l’histone acétyltransférase (HAT) de levure Rtt109 en présence de ses chaperonnes (Asf1 ou Vps75). Dans un second temps, nous avons développé une méthode d’analyse des peptides isomériques des histones. Cette méthode combine la LC-MS/MS à haute résolution et un nouvel outil informatique appelé Iso-PeptidAce qui permet de déconvoluer les spectres mixtes de peptides isomériques. Nous avons évalué Iso-PeptidAce avec un mélange de peptides synthétiques isomériques. Nous avons également validé les performances de cette approche avec des histones isolées de cellules humaines érythroleucémiques (K562) traitées avec des inhibiteurs d’histones désacétylases (HDACi) utilisés en clinique, et des histones de Saccharomyces cerevisiae liées au facteur d’assemblage de la chromatine (CAF-1) purifiées par chromatographie d’affinité. Enfin, en utilisant la méthode présentée précédemment, nous avons fait une analyse approfondie de la spécificité de plusieurs HATs et HDACs chez Schizosaccharomyces pombe. Nous avons donc déterminé les niveaux d’acétylation d’histones purifiées à partir de cellules contrôles ou de souches mutantes auxquelles il manque une HAT ou HDAC. Notre analyse nous a permis de valider plusieurs cibles connues des HATs et HDACs et d’en identifier de nouvelles. Nos données ont également permis de définir le rôle des différentes HATs et HDACs dans le maintien de l’équilibre d’acétylation des histones. Dans l’ensemble, nous anticipons que les méthodes décrites dans cette thèse permettront de résoudre certains défis rencontrés dans l’étude de la chromatine. De plus, ces données apportent de nouvelles connaissances pour l’élaboration d’études génétiques et biochimiques utilisant S. pombe.

ANALYSIS, MODIFICATION, AND EVALUATION OF THE COLD FLOW PROPERTIES OF VEGETABLE OILS AS BASE OIL FOR INDUSTRIAL LUBRICANTS

Poor cold flow properties of vegetable oils are a major problem preventing the usage of many abundantly available vegetable oils as base stocks for industrial lubricants. The major objective of this research is to improve the cold flow properties of vegetable oils by various techniques like additive addition and different chemical modification processes. Conventional procedure for determining pour point is ASTM D97 method. ASTM D97 method is time consuming and reproducibility of pour point temperatures is poor between laboratories. Differential Scanning Calorimetry (DSC) is a fast, accurate and reproducible method to analyze the thermal activities during cooling/heating of oil. In this work coconut oil has been chosen as representative vegetable oil for the analysis and improvement cold flow properties since it is abundantly available in the tropics and has a very high pour point of 24 °C. DSC is used for the analysis of unmodified and modified vegetable oil. The modified oils (with acceptable pour points) were then subjected to different tests for the valuation of important lubricant properties such as viscometric, tribological (friction and wear properties), oxidative and corrosion properties.A commercial polymethacrylate based PPD was added in different percentages and the pour points were determined in each case. Styrenated phenol(SP) was added in different concentration to coconut oil and each solution was subjected to ASTM D97 test and analysis by DSC. Refined coconut oil and other oils like castor oil, sunflower oil and keranja oil were mixed in different proportions and interesterification procedure was carried out. Interesterification of coconut oil with other vegetable oils was not found to be effective in lowering the pour point of coconut oil as the reduction attained was only to the extent of 2 to 3 °C.Chemical modification by acid catalysed condensation reaction with coconut oil castor oil mixture resulted in significant reduction of pour point (from 24 ºC to -3 ºC). Instead of using triacylglycerols, when their fatty acid derivatives (lauric acid- the major fatty acid content of coconut oil and oleic acid- the major fatty acid constituents of monoand poly- unsaturated vegetable oils like olive oil, sunflower oil etc.) were used for the synthesis , the pour point could be brought down to -42 ºC. FTIR and NMR spectroscopy confirmed the ester structure of the product which is fundamental to the biodegradability of vegetable oils. The tribological performance of the synthesised product with a suitable AW/EP additive was comparable to the commercial SAE20W30 oil. The viscometric properties (viscosity and viscosity index) were also (with out additives) comparable to commercial lubricants. The TGA experiment confirmed the better oxidative performance of the product compared to vegetable oils. The sample passed corrosion test as per ASTM D130 method.

Recurrence Quantification Analysis of System Signals for Detecting Tool and Chatter in Turning

In this thesis, the applications of the recurrence quantification analysis in metal cutting operation in a lathe, with specific objective to detect tool wear and chatter, are presented.This study is based on the discovery that process dynamics in a lathe is low dimensional chaotic. It implies that the machine dynamics is controllable using principles of chaos theory. This understanding is to revolutionize the feature extraction methodologies used in condition monitoring systems as conventional linear methods or models are incapable of capturing the critical and strange behaviors associated with the metal cutting process.As sensor based approaches provide an automated and cost effective way to monitor and control, an efficient feature extraction methodology based on nonlinear time series analysis is much more demanding. The task here is more complex when the information has to be deduced solely from sensor signals since traditional methods do not address the issue of how to treat noise present in real-world processes and its non-stationarity. In an effort to get over these two issues to the maximum possible, this thesis adopts the recurrence quantification analysis methodology in the study since this feature extraction technique is found to be robust against noise and stationarity in the signals.The work consists of two different sets of experiments in a lathe; set-I and set-2. The experiment, set-I, study the influence of tool wear on the RQA variables whereas the set-2 is carried out to identify the sensitive RQA variables to machine tool chatter followed by its validation in actual cutting. To obtain the bounds of the spectrum of the significant RQA variable values, in set-i, a fresh tool and a worn tool are used for cutting. The first part of the set-2 experiments uses a stepped shaft in order to create chatter at a known location. And the second part uses a conical section having a uniform taper along the axis for creating chatter to onset at some distance from the smaller end by gradually increasing the depth of cut while keeping the spindle speed and feed rate constant.The study concludes by revealing the dependence of certain RQA variables; percent determinism, percent recurrence and entropy, to tool wear and chatter unambiguously. The performances of the results establish this methodology to be viable for detection of tool wear and chatter in metal cutting operation in a lathe. The key reason is that the dynamics of the system under study have been nonlinear and the recurrence quantification analysis can characterize them adequately.This work establishes that principles and practice of machining can be considerably benefited and advanced from using nonlinear dynamics and chaos theory.

Capillary electrophoresis characterisation of a rapid prototyped PMMA chip for particle analysis

Màster en Nanociència i Nanotecnologia

Artificial neural network modeling for surface roughness prediction in cylindrical grinding of Al‐SiCp metal matrix composites and ANOVA analysis

Metal matrix composites (MMC) having aluminium (Al) in the matrix phase and silicon carbide particles (SiCp) in reinforcement phase, ie Al‐SiCp type MMC, have gained popularity in the re‐cent past. In this competitive age, manufacturing industries strive to produce superior quality products at reasonable price. This is possible by achieving higher productivity while performing machining at optimum combinations of process variables. The low weight and high strength MMC are found suitable for variety of components

Combined Analysis of the Short-Term Effects of Photochemical Air Pollutants on Mortality within the EMECAM Project

In recent years, some epidemiologic studies have attributed adverse effects of air pollutants on health not only to particles and sulfur dioxide but also to photochemical air pollutants (nitrogen dioxide and ozone). The effects are usually small, leading to some inconsistencies in the results of the studies. Furthermore, the different methodologic approaches of the studies used has made it difficult to derive generic conclusions. We provide here a quantitative summary of the short-term effects of photochemical air pollutants on mortality in seven Spanish cities involved in the EMECAM project, using generalized additive models from analyses of single and multiple pollutants. Nitrogen dioxide and ozone data were provided by seven EMECAM cities (Barcelona, Gijón, Huelva, Madrid, Oviedo, Seville, and Valencia). Mortality indicators included daily total mortality from all causes excluding external causes, daily cardiovascular mortality, and daily respiratory mortality. Individual estimates, obtained from city-specific generalized additive Poisson autoregressive models, were combined by means of fixed effects models and, if significant heterogeneity among local estimates was found, also by random effects models. Significant positive associations were found between daily mortality (all causes and cardiovascular) and NO2, once the rest of air pollutants were taken into account. A 10 μg/m3 increase in the 24-hr average 1-day NO2 level was associated with an increase in the daily number of deaths of 0.43% [95% confidence interval(CI), –0.003–0.86%] for all causes excluding external. In the case of significant relationships, relative risks for cause-specific mortality were nearly twice as much as that for total mortality for all the photochemical pollutants. Ozone was independently related only to cardiovascular daily mortality. No independent statistically significant relationship between photochemical air pollutants and respiratory mortality was found. The results in this study suggest that, given the present levels of photochemical pollutants, people living in Spanish cities are exposed to health risks derived from air pollution

Purification and electron cryomicroscopy of coronavirus particles

Intact, enveloped coronavirus particles vary widely in size and contour, and are thus refractory to study by traditional structural means such as X-ray crystallography. Electron microscopy (EM) overcomes some problems associated with particle variability and has been an important tool for investigating coronavirus ultrastructure. However, EM sample preparation requires that the specimen be dried onto a carbon support film before imaging, collapsing internal particle structure in the case of coronaviruses. Moreover, conventional EM achieves image contrast by immersing the specimen briefly in heavy-metal-containing stain, which reveals some features while obscuring others. Electron cryomicroscopy (cryo-EM) instead employs a porous support film, to which the specimen is adsorbed and flash-frozen. Specimens preserved in vitreous ice over holes in the support film can then be imaged without additional staining. Cryo-EM, coupled with single-particle image analysis techniques, makes it possible to examine the size, structure and arrangement of coronavirus structural components in fully hydrated, native virions. Two virus purification procedures are described.

Oxidation of biogenic and water-soluble compounds in aqueous and organic aerosol droplets by ozone: a kinetic and product analysis approach using laser Raman tweezers

The results of an experimental study into the oxidative degradation of proxies for atmospheric aerosol are presented. We demonstrate that the laser Raman tweezers method can be used successfully to obtain uptake coeffcients for gaseous oxidants on individual aqueous and organic droplets, whilst the size and composition of the droplets is simultaneously followed. A laser tweezers system was used to trap individual droplets containing an unsaturated organic compound in either an aqueous or organic ( alkane) solvent. The droplet was exposed to gas- phase ozone and the reaction kinetics and products followed using Raman spectroscopy. The reactions of three different organic compounds with ozone were studied: fumarate anions, benzoate anions and alpha pinene. The fumarate and benzoate anions in aqueous solution were used to represent components of humic- like substances, HULIS; a alpha- pinene in an alkane solvent was studied as a proxy for biogenic aerosol. The kinetic analysis shows that for these systems the diffusive transport and mass accommodation of ozone is relatively fast, and that liquid- phase di. ffusion and reaction are the rate determining steps. Uptake coe. ffcients, g, were found to be ( 1.1 +/- 0.7) x 10(-5), ( 1.5 +/- 0.7) x 10 (-5) and ( 3.0 - 7.5) x 10 (-3) for the reactions of ozone with the fumarate, benzoate and a- pinene containing droplets, respectively. Liquid- phase bimolecular rate coe. cients for reactions of dissolved ozone molecules with fumarate, benzoate and a- pinene were also obtained: k(fumarate) = ( 2.7 +/- 2) x 10 (5), k(benzoate) = ( 3.5 +/- 3) x 10 (5) and k(alpha-pinene) = ( 1-3) x 10(7) dm(3) mol (-1) s (- 1). The droplet size was found to remain stable over the course of the oxidation process for the HULIS- proxies and for the oxidation of a- pinene in pentadecane. The study of the alpha- pinene/ ozone system is the first using organic seed particles to show that the hygroscopicity of the particle does not increase dramatically over the course of the oxidation. No products were detected by Raman spectroscopy for the reaction of benzoate ions with ozone. One product peak, consistent with aqueous carbonate anions, was observed when following the oxidation of fumarate ions by ozone. Product peaks observed in the reaction of ozone with alpha- pinene suggest the formation of new species containing carbonyl groups.

A structural analysis of M protein in coronavirus assembly and morphology

The M protein of coronavirus plays a central role in virus assembly, turning cellular membranes into workshops where virus and host factors come together to make new virus particles. We investigated how M structure and organization is related to virus shape and size using cryo-electron microscopy, tomography and statistical analysis. We present evidence that suggests M can adopt two conformations and that membrane curvature is regulated by one M conformer. Elongated M protein is associated with rigidity, clusters of spikes and a relatively narrow range of membrane curvature. In contrast, compact M protein is associated with flexibility and low spike density. Analysis of several types of virus-like particles and virions revealed that S protein, N protein and genomic RNA each help to regulate virion size and variation, presumably through interactions with M. These findings provide insight into how M protein functions to promote virus assembly.

A simple analysis of thermodynamic properties for classical plasmas: I. theory

By eliminating the short range negative divergence of the Debye–Hückel pair distribution function, but retaining the exponential charge screening known to operate at large interparticle separation, the thermodynamic properties of one-component plasmas of point ions or charged hard spheres can be well represented even in the strong coupling regime. Predicted electrostatic free energies agree within 5% of simulation data for typical Coulomb interactions up to a factor of 10 times the average kinetic energy. Here, this idea is extended to the general case of a uniform ionic mixture, comprising an arbitrary number of components, embedded in a rigid neutralizing background. The new theory is implemented in two ways: (i) by an unambiguous iterative algorithm that requires numerical methods and breaks the symmetry of cross correlation functions; and (ii) by invoking generalized matrix inverses that maintain symmetry and yield completely analytic solutions, but which are not uniquely determined. The extreme computational simplicity of the theory is attractive when considering applications to complex inhomogeneous fluids of charged particles.

On the quantum mechanical scattering statistics of many particles

The probability of a quantum particle being detected in a given solid angle is determined by the S-matrix. The explanation of this fact in time-dependent scattering theory is often linked to the quantum flux, since the quantum flux integrated against a (detector-) surface and over a time interval can be viewed as the probability that the particle crosses this surface within the given time interval. Regarding many particle scattering, however, this argument is no longer valid, as each particle arrives at the detector at its own random time. While various treatments of this problem can be envisaged, here we present a straightforward Bohmian analysis of many particle potential scattering from which the S-matrix probability emerges in the limit of large distances.

A thermoresponsive supramolecular polymer network comprising pyrene-functionalized gold nano-particles and a chain-folding polydiimide.

A thermoresponsive, supramolecular nanocomposite has been prepared by the addition of pyrenyl functionalized gold nanoparticles (AuNPs) to a polydiimide that contains receptor residues designed to form defined complexes with pyrene. The novel pyrenyl-functionalized AuNPs (P-AuNPs) were characterized by transmission electron microscopy, with surface functionalization confirmed by infrared and UV–visible spectroscopic analyses. Mixing solutions of the P-AuNPs and a π-electron-deficient polydiimide resulted in the formation of electronically complementary, chain-folded and π–π-stacked complexes, so affording a new supramolecular nanocomposite network which precipitated from solution. The P-AuNPs bind to the polydiimide via π–π stacking interactions to create supramolecular cross-links. UV–visible spectroscopic analysis confirmed the thermally reversible nature of the complexation process, and transmission electron microscopy (TEM), infrared spectroscopy (IR), and differential scanning calorimetry (DSC) were used to characterize the supramolecular-nanocomposite material. The supramolecular polymer network is insoluble at room temperature, yet may be dissolved at temperatures above 60 °C. The thermal reversibility of this system is maintained over five heat/cool cycles without diminishment of the network characteristics. In contrast to the individual components, the nanocomposite formed self-supporting films, demonstrating the benefit of the supramolecular network in terms of mechanical properties. Control experiments probing the interactions between a model diimide compound that can also form a π-stacked complex with the π-electron rich pyrene units on P-AuNPs showed that, while complexation was readily apparent, precipitation did not occur because a supramolecular cross-linked network system could not be formed with this system.

Purification of coronavirus virions for Cryo-EM and proteomic analysis

Purification of intact enveloped virus particles can be useful as a first step in understanding the structure and function of both viral and host proteins that are incorporated into the virion. Purified preparations of virions can be used to address these questions using techniques such as mass spectrometry proteomics. Recent studies on the proteome of coronavirus virions have shown that in addition to the structural proteins, accessory and non-structural virus proteins and a wide variety of host cell proteins associate with virus particles. To further study the presence of virion proteins, high quality sample preparation is crucial to ensure reproducible analysis by the wide variety of methods available for proteomic analysis.

Characterization of virus-like particles associated with the human faecal and caecal microbiota

This work represents an investigation into the presence, abundance and diversity of virus-like particles (VLPs) associated with human faecal and caecal samples. Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery. The applicability of the developed VLP characterization method beyond the use of faecal samples was then verified using samples obtained from human caecal fluid.