The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

Reactive processing of polymers:functionalisation of ethylene-propylene diene terpolymer (EPDM) in the presence and absence of a co-agent and effect of functionalised EPDM on compatibilisation of poly(ethylene terephthalate)/EPDM blends

Ethylene-propylene diene terpolymer (EPDM) was functionalized with glycidyl methacrylate (GMA) during melt processing by free radical grafting with peroxide initiation in the presence and absence of a reactive comonomer trimethylolpropane triacrylate (Tris). Increasing the peroxide concentration resulted in an increase in the GMA grafting yield, albeit the overall grafting level was low and was accompanied by higher degree of crosslinking of EPDM which was found to be the major competing reaction. The presence of Tris in the grafting system gave rise to higher grafting yield produced at a much lower peroxide concentration though the crosslinking reactions remained high but without the formation of GMA-homopolymer in either of the two systems. The use of these functionalized EPDM (f-EPDM) samples with PET as compatibilisers in binary and ternary blends of PET/EPDM/f-EPDM was evaluated. The influence of the different functionalisation routes of the rubber phase (in presence and absence of Tris) and the effect of the level of functionality and microstructure of the resultant f-EPDM on the extent of the interfacial reaction, morphology and mechanical properties was also investigated. It is suggested that the mechanical properties of the blends are strongly influenced by the performance of the graft copolymer, which is in turn, determined by the level of functionality, molecular structure of the functionalized rubber and the interfacial concentration of the graft copolymer across the interface. The cumulative evidence obtained from torque rheometry, scanning electron microscopy, SEM, dynamic mechanical analysis (DMA), tensile mechanical tests and Fourier transform infrared (FTIR) supports this. It was shown that binary and ternary blends prepared with f-EPDM in the absence of Tris and containing lower levels of g-GMA effected a significant improvement in mechanical properties. This increase, particularly in elongation to break, could be accounted for by the occurrence of a reaction between the epoxy groups of GMA and the hydroxyl/carboxyl end groups of PET that would result in a graft copolymer which could, most probably, preferentially locate at the interface, thereby acting as an 'emulsifier' responsible for decreasing the interfacial tension between the otherwise two immiscible phases. This is supported by results from FTIR analysis of the fractionated PET phase of these blends which confirm the formation of an interfacial reaction, DMA results which show a clear shift in the T s of the blend components and SEM results which reveal very fine morphology, suggesting effective compatibilisation that is concomitant with the improvement observed in their tensile properties. Although Tris has given rise to highest amount of g-GMA, it resulted in lower mechanical properties than the optimized blends produced in the absence of Tris. This was attributed to the difference in the microstructure of the graft and the level of functionality in these samples resulting in less favourable structure responsible for the coarser dispersion of the rubber phase observed by SEM, the lower extent of T shift of the PET phase (DMA), the lower height of the torque curve during reactive blending and FTIR analysis of the separated PET phase that has indicated a lower extent of the interfacial chemical reaction between the phases in this Tris-containing blend sample. © 2005 Elsevier Ltd. All rights reserved.

Operando synchronous DRIFTS/MS/XAS as a powerful tool for guiding the design of Pd catalysts for the selective oxidation of alcohols

The selective aerobic oxidation of crotyl alcohol to crotonaldehyde was investigated by time-resolved synchronous DRIFTS/MS/XAS over silica and alumina supported Pd nanoparticles. Alcohol and oxygen reactant feeds were cycled through the catalyst bed while dynamic measurements of the palladium oxidation state, molecular adsorbates and evolved product distribution were made simultaneously on a sub-second timescale. Highly dispersed palladium nanoparticles remained in a partially oxidised state

Rational design of heterogeneous catalysts for biodiesel synthesis

Dwindling oil reserves and growing concerns over carbon dioxide emissions and associated climate change are driving the utilisation of renewable feedstocks as alternative, sustainable fuel sources. Catalysis has a rich history of facilitating energy efficient, selective molecular transformations, and contributes to 90% of current chemical manufacturing processes. In a post-petroleum era, catalysis will be pivotal in overcoming the scientific and engineering barriers to economically feasible bio-fuels. This perspective highlights some recent developments in heterogeneous catalysts for the synthesis of biodiesel from renewable resources, derived from plant and aquatic oil sources. Particular attention will be paid to the importance of catalyst pore architecture, surface polarity and acid and base properties, in meeting the challenge of transforming highly polar and viscous bio-based reactants. © 2012 The Royal Society of Chemistry.

The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

Pseudoperiodic "Living" and/or controlled cationic ring-opening copolymerization of oxetane with tetrahydropyran:microstructure of polymers vs kinetics of chain growth

The "living" and/or controlled cationic ring-opening bulk copolymerization of oxetane (Ox) with tetrahydropyran (THP) (cyclic ether with no homopolymerizability) at 35°C was examined using ethoxymethyl-1 -oxoniacyclohexane hexafluoroantimonate (EMOA) and (BF3 · CH3OH)THP as fast and slow initiator, respectively, yielding living and nonliving polymers with pseudoperiodic sequences (i.e., each pentamethylene oxide fragment inserted into the polymer is flanked by two trimethylene oxide fragments). Good control over number-average molecular weight (Mn up to 150000 g mol-1) with molecular weight distribution (MWD ∼ 1.4-1, 5) broader than predicted by the Poison distribution (MWDs > 1 +1/DPn) was attained using EMOA as initiating system, i.e., C 2H5OCH2Cl with 1.1 equiv of AgSbF6 as a stable catalyst and 1.1 equiv of 2,6-di-tert-butylpyridine used as a non-nucleophilic proton trap. With (BF3 · CH 3OH)THP, a drift of the linear dependence M n(GPC) vs Mn(theory) to lower molecular weight was observed together with the production of cyclic oligomers, ∼3-5% of the Ox consumed in THP against ∼30% in dichloromethane. Structural and kinetics studies highlighted a mechanism of chains growth where the rate of mutual conversion between "strain ACE species" (chain terminated by a tertiary 1-oxoniacyclobutane ion, Al) and "strain-free ACE species" (chain terminated by a tertiary 1-oxoniacyclohexane ion, Tl) depends on the rate at which Ox converts the stable species T1 (kind of "dormant" species) into a living "propagating" center A1 (i.e., k aapp[Ox]). The role of the THP solvent associated with the suspension of irreversible and reversible transfer reactions to polymer, when the polymerization is initiated with EMOA, was predicted by our kinetic considerations. The activation -deactivation pseudoequilibrium coefficient (Qt) was then calculated in a pure theoretical basis. From the measured apparent rate constant of Ox (kOxapp) and THP (kTHPapp = ka(endo)app) consumption, Qt and reactivity ratio (kp/kd, k a(endo)/ka(exo), and ks/ka(endo) were calculated, which then allow the determination of the transition rate constant of elementary step reactions that governs the increase of Mu with conversion. © 2009 American Chemical Society.

The design of contact lens based ocular drug delivery systems for single-day use:part (I) structural factors, surrogate ophthalmic dyes and passive diffusion studies

The poor retention and efficacy of instilled drops as a means of delivering drugs to the ophthalmic environment is well-recognised. The potential value of contact lenses as a means of ophthalmic drug delivery, and consequent improvement of pre-corneal retention is one obvious route to the development of a more effective ocular delivery system. Furthermore, the increasing availability and clinical use of daily disposable contact lenses provides the platform for the development of viable single-day use drug delivery devices based on existing materials and lenses. In order to provide a basis for the effective design of such devices, a systematic understanding of the factors affecting the interaction of individual drugs with the lens matrix is required. Because a large number of potential structural variables are involved, it is necessary to achieve some rationalisation of the parameters and physicochemical properties (such as molecular weight, charge, partition coefficients) that influence drug interactions. Ophthalmic dyes and structurally related compounds based on the same core structure were used to investigate these various factors and the way in which they can be used in concert to design effective release systems for structurally different drugs. Initial studies of passive diffusional release form a necessary precursor to the investigation of the features of the ocular environment that over-ride this simple behaviour. Commercially available contact lenses of differing structural classifications were used to study factors affecting the uptake of the surrogate actives and their release under 'passive' conditions. The interaction between active and lens material shows considerable and complex structure dependence, which is not simply related to equilibrium water content. The structure of the polymer matrix itself was found to have the dominant controlling influence on active uptake; hydrophobic interaction with the ophthalmic dye playing a major role. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

The development of biomaterials for contact lens applications:effects of wear modality on materials design

The successful design of polymers for contact lens applications depends on the ability to provide a balance of properties appropriate to the ocular environment. Principal relevant aspects of the anterior eye are the tear film, eyelid and cornea, which govern the requirements for surface properties, modulus and oxygen permeability, respectively. Permeability requirements and the developing view of the needs of the cornea, in terms of oxygen consumption and the particular roles of fluorine and silicon in the design of silicone hydrogels, which have proved to be the most successful family of materials for this demanding application, are discussed. The contact lens field is complicated by the fact that contact lenses are used in a range of wear modalities, the extremes of which can conveniently be classified as lenses that are disposed of at the end of a single period of daily wear and those used for 30. days of successive day-and-night periods, frequently referred to as extended or continuous wear. As silicone hydrogels developed, in the decade following their launch there has been a progressive trend in properties taking both modulus and water content closer to those of conventional hydrogels. This is particularly evident in the family of daily disposable contact lenses that have appeared since 2008.

Multi-objective optimization of the molecular structure of refrigerants

The aim of this work was to develop a new methodology, which can be used to design new refrigerants that are better than the currently used refrigerants. The methodology draws some parallels with the general approach of computer aided molecular design. However, the mathematical way of representing the molecular structure of an organic compound and the use of meta models during the optimization process make it different. In essence, this approach aimed to generate molecules that conform to various property requirements that are known and specified a priori. A modified way of mathematically representing the molecular structure of an organic compound having up to four carbon atoms, along with atoms of other elements such as hydrogen, oxygen, fluorine, chlorine and bromine, was developed. The normal boiling temperature, enthalpy of vaporization, vapor pressure, tropospheric lifetime and biodegradability of 295 different organic compounds, were collected from open literature and data bases or estimated. Surrogate models linking the previously mentioned quantities with the molecular structure were developed. Constraints ensuring the generation of structurally feasible molecules were formulated and used in commercially available optimization algorithms to generate molecular structures of promising new refrigerants. This study was intended to serve as a proof-of-concept of designing refrigerants using the newly developed methodology.

Design of binary polymeric systems containing ɩ-carrageenan and hydroxypropylcellulose for use in cataract surgery.

This study describes the design and characterisation of the rheological and mechanical properties of binary polymeric systems composed of 2-Hydroxypropylcellulose and ɩ-carrageenan, designed as ophthalmic viscoelastic devices (OVDs). Platforms were characterised using dilute solution, flow and oscillatory rheometry and texture profile analysis. Rheological synergy between the two polymers was observed both in the dilute and gel states. All platforms exhibited pseudoplastic flow. Increasing polymer concentrations significantly decreased the loss tangent and rate index yet increased the storage and loss moduli, consistency, gel hardness, compressibility and adhesiveness, the latter being related to the in-vivo retention properties of the platforms. Binary polymeric platforms exhibited unique physicochemical properties, properties that could not be engineered using mono-polymeric platforms. Using characterisation methods that provide information relevant to their clinical performance, low-cost binary platforms (3% hydroxypropylcellulose and either 1% or 2% ɩ-carrageenan) were identified that exhibited rheological, textural and viscoelastic properties advantageous for use as OVDs.

Design of Polyamine-Grafted Starches for Nucleotide Analogue Delivery: In Vitro Evaluation of the Anticancer Activity

International audience

Revisiting molecular diagnostics of Streptococcus pneumoniae

Streptococcus pneumoniae is a human pathobiont that colonizes the nasopharynx. S. pneumoniae is responsible for causing non-invasive and invasive disease such as otitis, pneumonia, meningitis, and sepsis, being a leading cause of infectious diseases worldwide. Due to similarities with closely related species sharing the same niche, it may be a challenge to correctly distinguish S. pneumoniae from its relatives when using only non-culture based methods such as real time PCR (qPCR). In 2007, a molecular method targeting the major autolysin (lytA) of S. pneumoniae by a qPCR assay was proposed by Carvalho and collaborators to identify pneumococcus. Since then, this method has been widely used worldwide. In 2013, the gene encoding for the ABC iron transporter lipoprotein PiaA, was proposed by Trzcinzki and collaborators to be used in parallel with the lytA qPCR assay. However, the presence of lytA gene homologues has been described in closely related species such as S. pseudopneumoniae and S. mitis and the presence of piaA gene is not ubiquitous between S. pneumoniae. The hyaluronate lyase gene (hylA) has been described to be ubiquitous in S. pneumoniae. This gene has not been used so far as a target for the identification of S. pneumoniae. The aims of our study were to evaluate the specificity, sensitivity, positive predicted value (PPV) and negative predicted value (NPV) of the lytA and piaA qPCR methods; design and implement a new assay targeting the hylA gene and evaluate the same parameters above described; analyze the assays independently and the possible combinations to access what is the best approach using qPCR to identify S. pneumoniae. A total of 278 previously characterized strains were tested: 61 S. pseudopneumoniae, 37 Viridans group strains, 30 type strains from other streptococcal species and 150 S. pneumoniae strains. The collection included both carriage and disease isolates. By Mulilocus Sequence Analysis (MLSA) we confirmed that strains of S. pseudopneumoniae could be misidentified as S. pneumoniae when lytA qPCR assay is used. The results showed that as a single target, lytA had the best combination of specificity, sensitivity, PPV and NPV being, 98.5%, 100.0%, 98.7% and 100.0% respectively. The combination of targets with the best values of specificity, sensibility, PPV and NPV were lytA and piaA, with 100.0%, 93.3%, 97.9% and 92.6%, respectively. Nonetheless by MLSA we confirmed that strains of S. pseudopneumoniae could be misidentified as S. pneumoniae and some capsulated (23F, 6B and 11A) and non-capsulated S. pneumoniae were not Identified using this assay. The hylA gene as a single target had the lowest PPV. Nonetheless it was capable to correctly identify all S. pneumoniae.

Design of functional hybrid coatings with anti-biofouling, self-cleaning and anti-reflecting applications

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Molecular Origins of Higher Harmonics in Large-Amplitude Oscillatory Shear Flow: Shear Stress Response

Recent work has focused on deepening our understanding of the molecular origins of the higher harmonics that arise in the shear stress response of polymeric liquids in large-amplitude oscillatory shear flow. For instance, these higher harmonics have been explained by just considering the orientation distribution of rigid dumbbells suspended in a Newtonian solvent. These dumbbells, when in dilute suspension, form the simplest relevant molecular model of polymer viscoelasticity, and this model specifically neglects interactions between the polymer molecules [R.B. Bird et al., J Chem Phys, 140, 074904 (2014)]. In this paper, we explore these interactions by examining the Curtiss-Bird model, a kinetic molecular theory designed specifically to account for the restricted motions that arise when polymer chains are concentrated, thus interacting and specifically, entangled. We begin our comparison using a heretofore ignored explicit analytical solution [Fan and Bird, JNNFM, 15, 341 (1984)]. For concentrated systems, the chain motion transverse to the chain axis is more restricted than along the axis. This anisotropy is described by the link tension coefficient, ε, for which several special cases arise: ε = 0 corresponds to reptation, ε > 1/8 to rod-climbing, 1/2 ≥ ε ≥ 3/4 to reasonable predictions for shear-thinning in steady simple shear flow, and ε = 1 to the dilute solution without hydrodynamic interaction. In this paper, we examine the shapes of the shear stress versus shear rate loops for the special cases ε = (0,1/8, 3/8,1) , and we compare these with those of rigid dumbbell and reptation model predictions.

Design of biobased additives for tuning the properties of biopolymers

This work mainly arises from the necessity to support the rapid introduction of different biobased polymers that the industrial sector has been facing lately. Indeed, while considerable efforts are being made to find environmentally and economically sustainable materials, less attention is paid to their need to be properly compounded to fulfil increasingly rigorous technical and quality requirements. Therefore, there is a strong demand for the development of a novel generation of compatible additives able to improve the properties of biobased polymers while respecting sustainability. With this in mind, a new class of biobased plasticizers is herein proposed. Five different ketal-diesters were selectively synthesized starting from levulinic acid, a promising renewable chemical platform. These molecules were added to poly(vinyl chloride) as model polymer to test their plasticizing effectiveness. Complete morphological, thermal and viscoelastic characterizations showed a clear correlation between the structural features of the ketal-esters and the properties of the material. In addition, no significant leaching was found in both hydrophilic and lipophilic environments. Importantly, the proposed ketal-diesters performed comparably and, in some cases, even better than commercial plasticizers. The same molecules were then added to bacterial poly(3-hydroxybutyrate), a semicrystalline polyester characterized by poor thermal and mechanical properties. Morphology assessments showed no phase separation and the plasticizing effectiveness was confirmed by thermal and viscoelastic analyses, while leaching tests showed low extraction values. Readily usable fractions with controlled structure and tailored properties were obtained from highly heterogeneous industrial grade Kraft lignin. These fractions were then added to poly(vinyl alcohol). Promising preliminary results in terms of compatibility were achieved, with thermograms showing only one glass transition temperature. Finally, a fully biobased glycerol-trilevulinate was successfully synthesized by means of a mild and solvent-free route. Its plasticizing effectiveness was evaluated on poly(vinyl chloride), showing a significant decrease of the glass transition temperature of the material.