Le projet organisant : vers une ontologie du projet d'aménagement

Codirection: Dr. Gonzalo Lizarralde

Biochemical effects of the pesticide Chlorpyrifos on the fish Oreochromis mossambicus (Peters)

Man uses a variety of synthetic material for his comfortable materialistic life. Thus human interactions may become harmful for various terrestrial and aquatic lives. This is by contaminating their habitat and by becoming a threat to organisms itself. Thus the application and dispersal of several organic pollutants can lead to the development of several mutated forms of the species when exposed to sublethal concentrations of the pollutants. Otherwise, a decrease in number or extinction of these exposed species from earth's face may happen. Pesticides, we use for the benefit of crop yield, but its persistence may become havoc to non-target organism. Pesticides reaching a reservoir can subsequently enter the higher trophic levels. Organophosphorus compounds have replaced all other pesticides, due to its acute toxicity and non-persistent nature.Hence the present study has concentrated on the toxicity of the largest market-selling and multipurpose pesticide, chlorpyrifos on the commonly edible aquatic organism, fish. The euryhaline cichlid Oreochromis mossambicus was selected as animal model. The study has concentrated on investigating biochemical parameters like tissue-specific enzymes, antioxidant and lipid-peroxidation parameters, haematological and histological observations and pesticide residue analysis.Major findings of this work have indicated the possibility of aquatic toxicity to the fish on exposure to the insecticide chlorpyrifos. The insecticide was found as effective to induce structural alteration, depletion in protein content, decrease in different metabolic enzyme levels and to progress lipid peroxidation on a prolonged exposure of 21 days. The ion-transport mechanism was found to be adversely affected. Electrophoretic analysis revealed the disappearance of several protein bands after 21days of exposure to chlorpyrifos. Residue, analysis by gas chromatography explored the levels of chlorpyrifos retaining on the edible tissue portions during exposure period of 21days and also on a recovery period of 10 days.

Design and study of self-assembled functional organic and hybrid systems for biological applications

The focus of self-assembly as a strategy for the synthesis has been confined largely to molecules, because of the importance of manipulating the structure of matter at the molecular scale. We have investigated the influence of temperature and pH, in addition to the concentration of the capping agent used for the formation of the nano-bio conjugates. For example, the formation of the narrower size distribution of the nanoparticles was observed with the increase in the concentration of the protein, which supports the fact that γ-globulin acts both as a controller of nucleation as well as stabiliser. As analyzed through various photophysical, biophysical and microscopic techniques such as TEM, AFM, C-AFM, SEM, DLS, OPM, CD and FTIR, we observed that the initial photoactivation of γ-globulin at pH 12 for 3 h resulted in small protein fibres of ca. Further irradiation for 24 h, led to the formation of selfassembled long fibres of the protein of ca. 5-6 nm and observation of surface plasmon resonance band at around 520 nm with the concomitant quenching of luminescence intensity at 680 nm. The observation of light triggered self-assembly of the protein and its effect on controlling the fate of the anchored nanoparticles can be compared with the naturally occurring process such as photomorphogenesis.Furthermore,our approach offers a way to understand the role played by the self-assembly of the protein in ordering and knock out of the metal nanoparticles and also in the design of nano-biohybrid materials for medicinal and optoelectronic applications. Investigation of the potential applications of NIR absorbing and water soluble squaraine dyes 1-3 for protein labeling and anti-amyloid agents forms the subject matter of the third chapter of the thesis. The study of their interactions with various proteins revealed that 1-3 showed unique interactions towards serum albumins as well as lysozyme. 69%, 71% and 49% in the absorption spectra as well as significant quenching in the fluorescence intensity of the dyes 1-3, respectively. Half-reciprocal analysis of the absorption data and isothermal titration calorimetric (ITC) analysis of the titration experiments gave a 1:1 stoichiometry for the complexes formed between the lysozyme and squaraine dyes with association constants (Kass) in the range 104-105 M-1. We have determined the changes in the free energy (ΔG) for the complex formation and the values are found to be -30.78, -32.31 and -28.58 kJmol-1, respectively for the dyes 1, 2 and 3. Furthermore, we have observed a strong induced CD (ICD) signal corresponding to the squaraine chromophore in the case of the halogenated squaraine dyes 2 and 3 at 636 and 637 nm confirming the complex formation in these cases. To understand the nature of interaction of the squaraine dyes 1-3 with lysozyme, we have investigated the interaction of dyes 1-3 with different amino acids. These results indicated that the dyes 1-3 showed significant interactions with cysteine and glutamic acid which are present in the side chains of lysozyme. In addition the temperature dependent studies have revealed that the interaction of the dye and the lysozyme are irreversible. Furthermore, we have investigated the interactions of these NIR dyes 1-3 with β- amyloid fibres derived from lysozyme to evaluate their potential as inhibitors of this biologically important protein aggregation. These β-amyloid fibrils were insoluble protein aggregates that have been associated with a range of neurodegenerative diseases, including Huntington, Alzheimer’s, Parkinson’s, and Creutzfeldt-Jakob diseases. We have synthesized amyloid fibres from lysozyme through its incubation in acidic solution below pH 4 and by allowing to form amyloid fibres at elevated temperature. To quantify the binding affinities of the squaraine dyes 1-3 with β-amyloids, we have carried out the isothermal titration calorimetric (ITC) measurements. The association constants were determined and are found to be 1.2 × 105, 3.6× 105 and 3.2 × 105 M-1 for the dyes, 1-3, respectively. To gain more insights into the amyloid inhibiting nature of the squaraine dyes under investigations, we have carried out thioflavin assay, CD, isothermal titration calorimetry and microscopic analysis. The addition of the dyes 1-3 (5μM) led to the complete quenching in the apparent thioflavin fluorescence, thereby indicating the destabilization of β-amyloid fibres in the presence of the squaraine dyes. Further, the inhibition of the amyloid fibres by the squaraine dyes 1-3, has been evidenced though the DLS, TEM AFM and SAED, wherein we observed the complete destabilization of the amyloid fibre and transformation of the fibre into spherical particles of ca. These results demonstrate the fact that the squaraine dyes 1-3 can act as protein labeling agents as well as the inhibitors of the protein amyloidogenesis. The last chapter of the thesis describes the synthesis and investigation of selfassembly as well as bio-imaging aspects of a few novel tetraphenylethene conjugates 4-6.Expectedly, these conjugates showed significant solvatochromism and exhibited a hypsochromic shift (negative solvatochromism) as the solvent polarity increased, and these observations were justified though theoretical studies employing the B3LYP/6-31g method. We have investigated the self-assembly properties of these D-A conjugates though variation in the percentage of water in acetonitrile solution due to the formation of nanoaggregates. Further the contour map of the observed fluorescence intensity as a function of the fluorescence excitation and emission wavelength confirmed the formation of J-type aggregates in these cases. To have a better understanding of the type of self-assemblies formed from the TPE conjugates 4-6, we have carried out the morphological analysis through various microscopic techniques such as DLS, SEM and TEM. 70%, we observed rod shape architectures having ~ 780 nm in diameter and ~ 12 μM in length as evidenced through TEM and SEM analysis. We have made similar observations with the dodecyl conjugate 5 at ca. 70% and 50% water/acetonitrile mixtures, the aggregates formed from 4 and 5 were found to be highly crystalline and such structures were transformed to amorphous nature as the water fraction was increased to 99%. To evaluate the potential of the conjugate as bio-imaging agents, we have carried out their in vitro cytotoxicity and cellular uptake studies though MTT assay, flow cytometric and confocal laser scanning microscopic techniques. Thus nanoparticle of these conjugates which exhibited efficient emission, large stoke shift, good stability, biocompatibility and excellent cellular imaging properties can have potential applications for tracking cells as well as in cell-based therapies. In summary we have synthesized novel functional organic chromophores and have studied systematic investigation of self-assembly of these synthetic and biological building blocks under a variety of conditions. The investigation of interaction of water soluble NIR squaraine dyes with lysozyme indicates that these dyes can act as the protein labeling agents and the efficiency of inhibition of β-amyloid indicate, thereby their potential as anti-amyloid agents.

Biochemical Characterization and Bio-evaluation of Collagen and Collagen Peptides Extracted and Purified from Fish Skin: In vitro and In vivo Studies on Antiarthritic and Wound Healing Properties

In fish processing plants, there is huge amount of skin that is left as the waste. When this skin is taken and processed into fish collagen, it will save large amount of money that is used for extraction of collagen from other animal s.Fish collagen can be used as an alternative to replace mammalian collagen, especially collagen extracted from bovine, when we consider the outbreak of bovine spongiform encephalopathy (BSE), transmissible spongiform encephalopathy (TSE) and the foot - and-mouth disease (FMD) issues. BSE and TSE are progressive neurological disorders affecting cattles caused by proteinacious infectious particles called prions.The study aims in producing collagen that has been extracted from fish skin to replace other animal collagen so as to overcome the problem of other animal collagen issues. Also the study utilized the abandoned fish waste produced by fish processing industry since bone, skin, fin and scales of fish can be a useful source of collagen.

Embodied Autonomy in Digital Ecosystems: From Bio-Inspired Agents to Cognitive Systems

This paper proposes to promote autonomy in digital ecosystems so that it provides agents with information to improve the behavior of the digital ecosystem in terms of stability. This work proposes that, in digital ecosystems, autonomous agents can provide fundamental services and information. The final goal is to run the ecosystem, generate novel conditions and let agents exploit them. A set of evaluation measures must be defined as well. We want to provide an outline of some global indicators, such as heterogeneity and diversity, and establish relationships between agent behavior and these global indicators to fully understand interactions between agents, and to understand the dependence and autonomy relations that emerge between the interacting agents. Individual variations, interaction dependencies, and environmental factors are determinants of autonomy that would be considered. The paper concludes with a discussion of situations when autonomy is a milestone

Cooperación Sur-Sur: Análisis de su impacto en la transformación del régimen internacional de la OCDE en materia de cooperación internacional

Las relaciones de cooperación Sur-Sur revoluciona las lógicas tradicionales que dieron base al régimen de la cooperación internacional expedido desde la OCDE. La diferencia entre los donantes llamados “DAC” y los socios “No-DAC” en referencia a los Estados miembros del Comité de Asistencia al Desarrollo establece dos lógicas de cooperación internacional que se contraponen en sus dinámicas pero comparten un objetivo: el desarrollo. Estos dos tipos de relaciones de cooperación se diferencian en cuatro aspectos: calidad de los actores implicados, dirección de la relación, tipo de intercambio y presencia o ausencia del Principio de Condicionalidad. A diferencia de las relaciones de cooperación Norte-Sur donde se establece una relación unidireccional entre el donante y el receptor, canal utilizado para el flujo crediticio y financiero (bien sea a través de créditos o de subvenciones), las relaciones de cooperación Sur-Sur establecen una relación bidireccional. Esta bidireccionalidad hace que la cooperación internacional se convierta en una herramienta de poder relativo para aquellos actores que carecían de peso en el sistema internacional. La carta fundamental de los Estados con economías emergentes será darle voz a aquellos que no la han tenido. A través de relaciones que se catalogan como asociaciones estratégicas, entre sujetos con un similar nivel de desarrollo, el Principio de Condicionalidad como rector de la relación de cooperación, desaparece. Asi, la formación del Grupo de Tareas para la Cooperación Sur-Sur adscrito al DAC es una muestra del cambio estructural del régimen de la cooperación internacional, y más aún, de las dinámicas tradicionales del sistema internacional.

Polimorfismos del gen Butirilcolinesterasa responsables de reacciones adversas en pacientes consumidores de “cocaína”

La butirilcolinesterasa humana (BChE; EC 3.1.1.8) es una enzima polimórfica sintetizada en el hígado y en el tejido adiposo, ampliamente distribuida en el organismo y encargada de hidrolizar algunos ésteres de colina como la procaína, ésteres alifáticos como el ácido acetilsalicílico, fármacos como la metilprednisolona, el mivacurium y la succinilcolina y drogas de uso y/o abuso como la heroína y la cocaína. Es codificada por el gen BCHE (OMIM 177400), habiéndose identificado más de 100 variantes, algunas no estudiadas plenamente, además de la forma más frecuente, llamada usual o silvestre. Diferentes polimorfismos del gen BCHE se han relacionado con la síntesis de enzimas con niveles variados de actividad catalítica. Las bases moleculares de algunas de esas variantes genéticas han sido reportadas, entre las que se encuentra las variantes Atípica (A), fluoruro-resistente del tipo 1 y 2 (F-1 y F-2), silente (S), Kalow (K), James (J) y Hammersmith (H). En este estudio, en un grupo de pacientes se aplicó el instrumento validado Lifetime Severity Index for Cocaine Use Disorder (LSI-C) para evaluar la gravedad del consumo de “cocaína” a lo largo de la vida. Además, se determinaron Polimorfismos de Nucleótido Simple (SNPs) en el gen BCHE conocidos como responsables de reacciones adversas en pacientes consumidores de “cocaína” mediante secuenciación del gen y se predijo el efecto delos SNPs sobre la función y la estructura de la proteína, mediante el uso de herramientas bio-informáticas. El instrumento LSI-C ofreció resultados en cuatro dimensiones: consumo a lo largo de la vida, consumo reciente, dependencia psicológica e intento de abandono del consumo. Los estudios de análisis molecular permitieron observar dos SNPs codificantes (cSNPs) no sinónimos en el 27.3% de la muestra, c.293A>G (p.Asp98Gly) y c.1699G>A (p.Ala567Thr), localizados en los exones 2 y 4, que corresponden, desde el punto de vista funcional, a la variante Atípica (A) [dbSNP: rs1799807] y a la variante Kalow (K) [dbSNP: rs1803274] de la enzima BChE, respectivamente. Los estudios de predicción In silico establecieron para el SNP p.Asp98Gly un carácter patogénico, mientras que para el SNP p.Ala567Thr, mostraron un comportamiento neutro. El análisis de los resultados permite proponer la existencia de una relación entre polimorfismos o variantes genéticas responsables de una baja actividad catalítica y/o baja concentración plasmática de la enzima BChE y algunas de las reacciones adversas ocurridas en pacientes consumidores de cocaína.

The distributed nature of pattern generalization

Resumen tomado de la publicaci??n

Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Coordination-driven self-assembly of a novel carbonato-bridged heteromolecular neutral nickel(II) triangle by atmospheric CO2 fixation

Formation of a quasi-symmetrical mu(3)-carbonato-bridged self-assembled heteromolecular triangle of Ni(II), [(mu(3)-CO3){Ni-2(salmeNH)(2)(NCS)(2)}[Ni(salmeNH(2))(2)]center dot Et2O center dot H2O (HsalmeNH = 2-[(3-methylamino-propylimino)-methyl]-phenol) involves atmospheric CO2 uptake in a neutral medium, by spontaneous self-reorganization of the starting mononuclear Ni(II)-Schiff-base complex, [Ni(salmeNH)(2)]. The environment around Ni(II) in two of the subunits is different from the third one. The starting complex, (Ni(salmeNH)(2)], and one of the possible intermediate species, [Ni(salmeNH(2))(2)(NCS)(2)], which has a very similar coordination environment to that in the third Ni(II) center, have been characterized structurally. A plausible mechanism for the formation of such a triangle has also been proposed. The compound shows a very strong antiferromagnetic coupling. Fit as a regular triangular arrangement gave J = -53.1, g = 2.24, and R = 1.5 x 10(-4).

Self-esteem and coping in children with developmental coordination disorder

This study investigated self-esteem in children with developmental coordination disorder (DCD). Fifteen children between the ages of 8 and 12 years diagnosed with DCD were compared with a typically developing group comprising 30 children with average and good motor abilities, using measures of perceived competence, social support and self-esteem. The types of coping strategy generated in response to example vignettes were also compared. There was no significant difference between the groups in global self-esteem, but the children with DCD reported lower athletic and scholastic competence than their typically developing peers. No difference was found between the groups in level of perceived social support. The DCD group generated fewer coping strategies overall, but more passive and avoidant strategies than the typically developing children. The implications of the study are discussed with regard to future research directions, such as the investigation of the effects of motor skill intervention on self-esteem and the development of strategies to protect children's self-esteem.

Self-assembled molecular complexes and coordination polymers of CdII, hexamine, and monocarboxylates: structural analysis and theoretical studies of supramolecular interactions

Four new cadmium(II) complexes [Cd-2(bz)(4)(H2O)(4)(mu 2-hmt)]center dot Hbz center dot H2O (1), [Cd-3(bz)(6)(H2O)(6)(mu 2-hmt)(2)]center dot 6H(2)O (2), [Cd(pa)(2)(H2O)(mu(2)-hmt)](n) (3), and {[Cd-3(ac)(6)(H2O)(3)(mu(3)-hmt)(2)]center dot 6H(2)O}(n) (4) with hexamine (hmt) and monocarboxylate ions, benzoate (bz), phenylacetate (pa), or acetate (ac) have been synthesized and characterized structurally. Structure determinations reveal that 1 is dinuclear, 2 is trinuclear, 3 is a one-dimensional (1D) infinite chain, and 4 is a two-dimensional (2D) polymer with fused hexagonal rings consisting of Cd-II and hmt. All the Cd-II atoms in the four complexes (except one CdII in 2) possess seven-coordinate pentagonal bipyramidal geometry with the various chelating bidentate carboxylate groups in equatorial sites. One of the CdII ions in 2, a complex that contains two monodentate carboxylates is in a distorted octahedral environment. The bridging mode of hmt is mu 2- in complexes 1-3 but is mu 3- in complex 4. In all complexes, there are significant numbers of H-bonds, C-H/pi, and pi-pi interactions which play crucial roles in forming the supramolecular networks. The importance of the noncovalent interactions in terms of energies and geometries has been analyzed using high level ab initio calculations. The effect of the cadmium coordinated to hmt on the energetic features of the C-H/pi interaction is analyzed. Finally, the interplay between C-H/pi and pi-pi interactions observed in the crystal structure of 3 is also studied.