Analytical strategies for the comprehensive profiling of histone post translational modifications by mass spectrometry and implications for functional analyses

Le long bio-polymère d'ADN est condensé à l’intérieur du noyau des cellules eukaryotes à l'aide de petites protéines appelées histones. En plus de leurs fonctions condensatrices,ces histones sont également la cible de nombreuses modifications post-traductionnelles(MPT), particulièrement au niveau de leur section N-terminale. Ces modifications réversibles font partie d’un code d’histones épi-génétique transmissible qui orchestre et module dynamiquement certains événements impliquant la chromatine, tels l’activation et la désactivation de gènes ainsi que la duplication et la réparation d’ADN. Ces modifications sont impliquées subséquemment dans la signalisation et la progression de cancers, tels que la leucémie. En conséquence, l'élucidation des modifications d’histones est importante pour comprendre leurs fonctions biologiques. Une méthodologie analytique a été mise au point en laboratoire pour isoler, détecter, et quantifier les MPT d’histones en utilisant une approche rapide à deux volets à l’aide d’outils bioinformatiques spécialisés. La méthodologie développée en laboratoire a été validée en utilisant des histones de souche sauvage ainsi que deux types d’histones mutants déficients en enzymes acétyltransferase. Des trois sources d’histones utilisées, la seule MPT qui a démontré un changement significatif est l’acétylation de l’histone H3 à lysine 56 (H3K56ac). L’expression et la stoechiométrie de cette MPT, issue de cellules de souche sauvage et de cellules mutantes, ont été déterminées avec précision et comparées. Les fonctions de balayage polyvalentes d'un instrument à trappe ionique quadrupôle linéaire hybride ont été utilisées pour améliorer la détection de protéines intactes. Le mode de balayage « enhanced multiply charged » (EMC) a été modifié pour contenir et détecter les ions de protéines intactes situées dans la trappe ionique linéaire. Ce mode de balayage nommé « targeted EMC » (tEMC) a permis de quadrupler le niveau de sensibilité (signal/interférence), et quintupler la résolution du mode de balayage conventionnel. De plus, la capacité de séparation des charges du tEMC a réduit de façon significative les effets de « space charge » dans la trappe ionique linéaire. La résolution supérieure du mode tEMC a permis de différencier plusieurs isoformes modifiées, particulièrement pour l’histone H3. L’analyse des peptides d’histones trypsiques à l’aide du mode de balayage « MRM » a permis le séquençage et la quantification de MPT avec un haut degré de précision. La seule MPT qui était sous-exprimée entre l’histone de souche sauvage et le mutant DOT1L fut la méthylation de l’histone H3 lysine 79(H3K79me1). Les effets de deux inhibiteurs d’enzymes HDAC (HDACi) sur l’expression de MPT d’histone ont été évalués en utilisant la méthodologie analytique mentionnée. Les histones extraites de cellules normales et cancéreuses ont été exposées à du Vorinostat(SAHA) ou du Entinostat (MS-275) pour une période de 24 à 72 heures. Deux histones furent principalement affectées, soit H3 et H4. Étonnamment, les mêmes effets n'ont pas été détectés lorsque les cellules normales ont été traitées avec le HDACi pour une période de 48 à 72 heures. Une méthode absolue de quantification avec une courbe d’étalonnage a été développée pour le peptide H3K56ac. Contrairement à certaines publications, nos résultats démontrent que cette MPT est présente dans les cellules mammifères avec une stoechiométrie très basse (< 0,1%) et n'est pas surexprimée de façon significative après le traitement au HDACi.

Sol-Gel Mesoporous Silica Aerogels and Bio Hybrids for Functional Applications

The thesis covers a systematic investigation on the synthesis of silica aerogels and microspheres with tailored porosity, at ambient conditions by varying the experimental parameters as well as using organic templates. Organically modified silica-gelatin and silica-chitosan hybrids were developed for the first time using alkylalkoxysilanes such as MTMS and VTMS. Application of novel silica-biopolymer antiwetting coatings on different substrates such as glass, leather and textile is also demonstrated in the thesis.

Biocompatibility Study Of Hydroxyapatite-Chitosan Composite For Medical Applications At Microwave Frequencies

Hydroxyapatite (HAp, Ca10(PO4)6(OH)2) bioceramic and chitosan (poly [( -1-4) D-glucosamine]) biopolymer show good biocompatibility in vivo. They have biological origin and show excellent interactions with microwave. Microwave study of HAp made using different drying techniques and their composites with chitosan in the ISM band is presented. Pastes are made using HAp and chitosan with different ratios of mixing. The dielectric properties of this composites match with that of human fat, collagen tissues. Some of the compositions exhibit dielectric property close to that of natural bone. This makes them more biocompatible and better substitutes for natural bone. Thus composite bioceramics can be considered as phantom model constituents for imaging purposes. Their dielectric properties prove that they are biocompatible.

A Comparative Study of Fiber Optic Humidity Sensors Based on Chitosan and Agarose

A comparative study of two biopolymer based fiber optic humidity sensors is presented in this paper. Sensing elements Agarose and Chitosan swells in the presence of water vapour and undergoes changes in refractive index and modulates the intensity of light propagating through a fiber with Agarose or Chitosan as cladding.

Characterization of polyhydroxyalkanoates accumulating vibrios from marine benthic environments and production studies of polyhydroxyalkanoates by Vibrio sp. BTKB33

The present work deals with the characterization of polyhydroxyalkanoates accumulating vibrios from marine benthic environments and production studies of polyhydroxyalkanoates by vibrio sp.BTKB33. Vibrios are a group of (iram negative, curved or straight motile rods that normally inhabit the aquatic environments.The present study therefore aimed at evaluating the occurrence of PHA accumulating vibrios inhabiting marine benthic environments; characterizing the potential PHA accumulators employing phenotypic and genotypic approaches and molecular characterization of the PHA synthase gene. The study also evaluated the PHA production in V:'hri0 sp. strain BTKB33, through submerged fennentation using statistical optimization and characterized the purified biopolymer. Screening for PHA producing vibrios from marine benthic environments. Characterization of PHA producers employing phenotypic and genotypic approaches.The incidence of PHA accumulation in Vibrio sp. isolated from marine sediments was observed to be high, indicating that the natural habitat of these bacteria are stressful. Considering their ubiquitous nature, the ecological role played by vibrios in maintaining the delicate balance of the benthic ecosystem besides returning potential strains, with the ability to elaborate a plethora of extracellular enzymes for industrial application, is significant. The elaboration of several hydrolytic enzymes by individuals also emphasize the crucial role of vibrios in the mineralization process in the marine environment. This study throws light on the extracellular hydrolytic enzyme profile exhibited by vibrios. It was concluded that apart from the PHA accumulation, presence of exoenzyme production and higher MAR index also aids in their survival in the highly challenging benthic enviromnents. The phylogenetic analysis of the strains and studies on intra species variation within PHA accumulating strains reveal their diversity. The isolate selected for production in this study was Vibrio sp. strain BTKB33, identified as V.azureus by 16S rDNA sequencing and phenotypic characterization. The bioprocess variables for PHA production utilising submerged fermentation was optimized employing one-factor-at-a-time-method, PB design and RSM studies. The statistical optimization of bioprocess variables revealed that NaCl concentration, temperature and incubation period are the major bioprocess variables influencing PHA production and PHA content. The presence of Class I PHA synthase genes in BTKB33 was also unveiled. The characterization of phaC genes by PCR and of the extracted polymer employing FTIR and NMR analysis revealed the presence of polyhydroxybutyrate, smallest known PI-IAs, having wider domestic, industrial and medical application. The strain BTKB33 bearing a significant exoenzyme profile, can thus be manipulatedin future for utilization of diverse substrates as C- source for PHA production. In addition to BTKB33, several fast growing Vibrio sp. having PHA accumulating ability were also isolated, revealing the prospects of this environment as a mine for novel PHA accumulating microbes. The findings of this study will provide a reference for further research in industrial production of PHAs from marine microorganisms .

Ionomer Compatibilized Low Density Polyethylene - Tapioca Starch Blends Biodegradability and Photodegradability

Biodegradation is the chemical degradation of materials brought about by the action of naturally occurring microorganisms. Biodegradation is a relatively rapid process under suitable conditions of moisture, temperature and oxygen availability. The logic behind blending biopolymers such as starch with inert polymers like polyethylene is that if the biopolymer component is present in sufficient amount, and if it is removed by microorganisms in the waste disposal environment, then the base inert plastic should slowly degrade and disappear. The present work focuses on the preparation of biodegradable and photodegradable blends based on low density polyethylene incorporating small quantities of ionomers as compatibilizers. The thesis consists of eight chapters. The first chapter presents an introduction to the present research work and literature survey. The details of the materials used and the experimental procedures undertaken for the study are described in the second chapter. Preparation and characterization of low density polyethylene (LDPE)-biopolymer (starch/dextrin) blends are described in the third chapter. The result of investigations on the effect of polyethylene-co-methacrylic acid ionomers on the compatibility of LDPE and starch are reported in chapter 4. Chapter 5 has been divided into two parts. The first part deals with the effect of metal oxides on the photodegradation of LDPE. The second part describes the function of metal stearates on the photodegradation of LDPE. The results of the investigations on the role of various metal oxides as pro-oxidants on the degradation of ionomer compatibilized LDPE-starch blends are reported in chapter 6. Chapter 7 deals with the results of investigations on the role of various metal stearates as pro-oxidants on the degradation of ionomer compatibilized LDPE-starch blends. The conclusion of the investigations is presented in the last chapter of the thesis.

GABA and 5-HT chitosan nanoparticles enhanced liver cell proliferation and neuronal survival in partially hepatectomised rats: GABAB and 5-HT2A receptors functional

Nanoparticulate drug delivery systems provide wide opportunities for solving problems associated with drug stability or disease states and create great expectations in the area of drug delivery (Bosselmann & Williams, 2012). Nanotechnology, in a simple way, explains the technology that deals with one billionth of a meter scale (Ochekpe, et al., 2009). Fewer side effects, poor bioavailability, absorption at intestine, solubility, specific delivery to site of action with good pharmacological efficiency, slow release, degradation of drug and effective therapeutic outcome, are the major challenges faced by most of the drug delivery systems. To a great extent, biopolymer coated drug delivery systems coupled with nanotechnology alleviate the major drawbacks of the common delivery methods. Chitosan, deacetylated chitin, is a copolymer of β-(1, 4) linked glucosamine (deacetylated unit) and N- acetyl glucosamine (acetylated unit) (Radhakumary et al., 2005). Chitosan is biodegradable, non-toxic and bio compatible. Owing to the removal of acetyl moieties that are present in the amine functional groups of chitin, chitosan is readily soluble in aqueous acidic solution. The solubilisation occurs through the protonation of amino groups on the C-2 position of D-glucosamine residues whereby polysaccharide is converted into polycation in acidic media. Chitosan interacts with many active compounds due to the presence of amine group in it. The presence of this active amine group in chitosan was exploited for the interaction with the active molecules in the present study. Nanoparticles of chitosan coupled drugs are utilized for drug delivery in eye, brain, liver, cancer tissues, treatment of spinal cord injury and infections (Sharma et al., 2007; Li, et a., 2009; Paolicelli et al., 2009; Cho et al., 2010). To deliver drugs directly to the intended site of action and to improve pharmacological efficiency by minimizing undesired side effects elsewhere in the body and decrease the long-term use of many drugs, polymeric drug delivery systems can be used (Thatte et al., 2005).

Antimicrobial activity of chitosan against vibrios from freshwater prawn Macrobrachium rosenbergii larval rearing systems

Chitosan is a biocompatible and biodegradable natural polymer with established antimicrobial properties against specific microorganisms. The present study demonstrates its antibacterial activity against 48 isolates of Vibrio species from prawn larval rearing systems. The antibacterial activity had a positive correlation with the concentration of chitosan. This work opens up avenues for using chitosan as a prophylactic biopolymer for protecting prawn larvae from vibriosis.

Inverse Metabolic Engineering of Synechocystis PCC 6803 for Improved Growth Rate and Poly-3-hydroxybutyrate Production

Synechocystis PCC 6803 is a photosynthetic bacterium that has the potential to make bioproducts from carbon dioxide and light. Biochemical production from photosynthetic organisms is attractive because it replaces the typical bioprocessing steps of crop growth, milling, and fermentation, with a one-step photosynthetic process. However, low yields and slow growth rates limit the economic potential of such endeavors. Rational metabolic engineering methods are hindered by limited cellular knowledge and inadequate models of Synechocystis. Instead, inverse metabolic engineering, a scheme based on combinatorial gene searches which does not require detailed cellular models, but can exploit sequence data and existing molecular biological techniques, was used to find genes that (1) improve the production of the biopolymer poly-3-hydroxybutyrate (PHB) and (2) increase the growth rate. A fluorescence activated cell sorting assay was developed to screen for high PHB producing clones. Separately, serial sub-culturing was used to select clones that improve growth rate. Novel gene knock-outs were identified that increase PHB production and others that increase the specific growth rate. These improvements make this system more attractive for industrial use and demonstrate the power of inverse metabolic engineering to identify novel phenotype-associated genes in poorly understood systems.

Exploring the Factors Affecting the Solubility of Chitosan in Water

We explore the role of crystallinity and inter- or intramolecular forces in chitosan for its solubility in water and demonstrate the expansion of its solubility to a wider pH range. Due to its semicrystalline nature, derived mainly from inter- and intramolecular hydrogen bonds, chitosan is water-soluble only at pH < 6. In acidic conditions, its amino groups can be partially protonated resulting in repulsion between positively charged macrochains, thereby allowing diffusion of water molecules and subsequent solvation of macromolecules. We show that chemical disruption of chitosan crystallinity by partial re-acetylation or physical disruption caused by the addition of urea and guanidine hydrochloride broadens the pH-solubility range for this biopolymer.

Why is Chitosan Mucoadhesive?

Chitosan is a biocompatible and biodegradable amino polysaccharide, which is soluble in aqueous solutions at pH < 6.5. It has been widely used for developing drug delivery systems because of its excellent mucoadhesive properties. Although many studies report on chitosan being mucoadhesive, the nature of interactions between chitosan and mucin remains poorly defined. Here, we have examined the role of primary amino groups and the role of electrostatic attraction, hydrogen bonding, and hydrophobic effects on aggregation of gastric mucin in the presence of chitosan. Reducing the number of amino groups through their half acetylation results in expansion of chitosan’s pH-solubility window up to pH 7.4 but also reduces its capacity to aggregate mucin. We demonstrated that electrostatic attraction forces between chitosan and gastric mucin can be suppressed in the presence of 0.2 mol/L sodium chloride; however, this does not prevent the aggregation of mucin particles in the presence of this biopolymer. The presence of 8 mol/L urea or 10% v/v ethanol in solutions also affects mucin aggregation in the presence of chitosan, demonstrating the role of hydrogen bonding and hydrophobic effects, respectively, in mucoadhesion.

Liquid crystal phase formation by biopolymers

This review discusses liquid crystal phase formation by biopolymers in solution. Lyotropic mesophases have been observed for several classes of biopolymer including DNA, peptides, polymer/peptide conjugates, glycopolymers and proteoglycans. Nematic or chiral nematic (cholesteric) phases are the most commonly observed mesophases, in which the rod-like fibrils have only orientational order. Hexagonal columnar phases are observed for several systems (DNA, PBLG, polymer/peptide hybrids) at higher concentration. Lamellar (smectic) phases are reported less often, although there are examples such as the layer arrangement of amylopectin side chains in starch. Possible explanations for the observed structures are discussed. The biological role of liquid crystal phases for several of these systems is outlined. Commonly, they may serve as a template to align fibrils for defined structural roles when the biopolymer is extruded and dried, for instance in the production of silk by spiders or silkworms, or of chitin in arthropod shells. In other cases, liquid crystal phase formation may occur in vivo simply as a consequence of high concentration, for instance the high packing density of DNA within cell nuclei.

Dynamics of shear-induced orientation transitions in block copolymers

This review discusses liquid crystal phase formation by biopolymers in solution. Lyotropic mesophases have been observed for several classes of biopolymer including DNA, peptides, polymer/peptide conjugates, glycopolymers and proteoglycans. Nematic or chiral nematic (cholesteric) phases are the most commonly observed mesophases, in which the rod-like fibrils have only orientational order. Hexagonal columnar phases are observed for several systems (DNA, PBLG, polymer/peptide hybrids) at higher concentration. Lamellar (smectic) phases are reported less often, although there are examples such as the layer arrangement of amylopectin side chains in starch. Possible explanations for the observed structures are discussed. The biological role of liquid crystal phases for several of these systems is outlined. Commonly, they may serve as a template to align fibrils for defined structural roles when the biopolymer is extruded and dried, for instance in the production of silk by spiders or silkworms, or of chitin in arthropod shells. In other cases, liquid crystal phase formation may occur in vivo simply as a consequence of high concentration, for instance the high packing density of DNA within cell nuclei.

Enhancing the crystallization and orientation of electrospinning poly (lactic acid) (PLLA) by combining with additives

PLLA is a thermoplastic biopolymer and can be used in industrial applications for medical and filtration applications. The brittleness of PLLA is attributed to slow crystallization rates and its glass transition temperature (Tg) is high (60 °C); for this reason, its applications are limited. The orientation, morphology, and crystal structure of the electrospun fibers was investigated by SEM, POM, DSC, FTIR, XRD, and SAXS. Combining with additives leads to a large decrease of fiber diameter, viscosity, and changes of fiber morphology and crystal structure compared to pure PLLA. DSC showed that the Tg of PLLA decreased about 15 °C and there was no change in relaxation enthalpy by the addition of plasticizer. FT-IR indicate a strong interaction between PLLA and additives; a new band appears in the PLLA blend at 1,756 cm−1 at room temperature as a crystalline band without any annealing. In addition, WAXD indicated that the intensities of the two peaks at (200/110) and (203) increased for the blend at room temperature without any annealing in comparison with PLLA; this means that PHB crystallizes in the amorphous region of PLLA. The POM experiments agree with the results from DSC, FTIR, and WAXS measurements, confirming that adding PHB results in an increase in the number of nuclei with much smaller spherulites and enhances the crystallization behavior of this material, thereby improving its potential for applications.

Synthesis of chitosan/hydroxyapatite membranes coated with hydroxycarbonate apatite for guided tissue regeneration purposes

Chitosan, which is a non-toxic, biodegradable and biocompatible biopolymer, has been widely researched for several applications in the field of biomaterials. Calcium phosphate ceramics stand out among the so-called bioceramics for their absence of local or systemic toxicity, their non-response to foreign bodies or inflammations, and their apparent ability to bond to the host tissue. Hydroxyapatite (HA) is one of the most important bioceramics because it is the main component of the mineral phase of bone. The aim of this work was to produce chitosan membranes coated with hydroxyapatite using the modified biomimetic method. Membranes were synthesized from a solution containing 2% of chitosan in acetic acid (weight/volume) via the solvent evaporation method. Specimens were immersed in a sodium silicate solution and then in a 1.5 SBF (simulated body fluid) solution. The crystallinity of the HA formed over the membranes was correlated to the use of the nucleation agent (the sodium silicate solution itself). Coated membranes were characterized by means of scanning electron microscopy - SEM, X-ray diffraction - XRD, and Fourier transform infrared spectroscopy - FTIR. The results indicate a homogeneous coating covering the entire surface of the membrane and the production of a semi-crystalline hydroxyapatite layer similar to the mineral phase of human bone. (C) 2010 Elsevier B.V. All rights reserved.