Non-coding RNAs: multi-tasking molecules in the cell

In the last years it has become increasingly clear that the mammalian transcriptome is highly complex and includes a large number of small non-coding RNAs (sncRNAs) and long noncoding RNAs (lncRNAs). Here we review the biogenesis pathways of the three classes of sncRNAs, namely short interfering RNAs (siRNAs), microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). These ncRNAs have been extensively studied and are involved in pathways leading to specific gene silencing and the protection of genomes against virus and transposons, for example. Also, lncRNAs have emerged as pivotal molecules for the transcriptional and post-transcriptional regulation of gene expression which is supported by their tissue-specific expression patterns, subcellular distribution, and developmental regulation. Therefore, we also focus our attention on their role in differentiation and development. SncRNAs and lncRNAs play critical roles in defining DNA methylation patterns, as well as chromatin remodeling thus having a substantial effect in epigenetics. The identification of some overlaps in their biogenesis pathways and functional roles raises the hypothesis that these molecules play concerted functions in vivo, creating complex regulatory networks where cooperation with regulatory proteins is necessary. We also highlighted the implications of biogenesis and gene expression deregulation of sncRNAs and lncRNAs in human diseases like cancer.

Reactivity of bulky tris(Phenylpyrazolyl) methanesulfonate copper(I) complexes towards small unsaturated molecules

Reaction of the tris(3-phenylpyrazolyl)methane sulfonate species (Tpms(Ph))Li with the copper(I) complex [Cu(MeCN)(4)][PF6] affords [Cu(Tpms(Ph))(MeCN)] 1. The latter, upon reaction with equimolar amounts of cyclohexyl-(CyNC) or 2,6-dimethylphenyl (XylNC) isocyanides, or excess CO, furnishes the corresponding Cu(I)complexes [Cu(Tpms(Ph))(CNR)] (R = Cy 2, Xyl 3) or [Cu(Tpms(Ph))(CO)] 4. The ligated isocyanide in 2 or 3 (or the acetonitrile ligand in 1)is displaced by 3-iminoisoindolin-1-one to afford 5, the first copper(I) complex containing an 3-iminoisoindolin-1-one ligand. The ligated acetonitrile in 1 undergoes nucleophilic attack by methylamine to give the amidine complex [Cu(Tpms(Ph)){MeC(NH)NHMe}] 6, whereas only the starting materials were recovered from the attempted corresponding reactions of 2 and 3 with methylamine. Complexes 1 or 6 form the trinuclear hydroxo-copper(II)species [(mu-Cu){Cu(mu-OH) (2)(Tpms(Ph))}(2)] 7 upon air oxidation in moist methanol. In all the complexes the scorpionate ligand facially caps the metal in the N,N,O-coordination mode.

Employment of the side product of biodiesel production in the formation of surfactant like molecules

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Química e Bioquímica

Regulatory RNA binding molecules : implication for diabetes pathogenesis

Le glucose est notre principale source d'énergie. Après un repas, le taux de glucose dans le sang (glycémie) augmente, ce qui entraine la sécrétion d'insuline. L'insuline est une hormone synthétisée au niveau du pancréas par des cellules dites bêta. Elle agit sur différents organes tels que les muscles, le foie ou le tissu adipeux, induisant ainsi le stockage du glucose en vue d'une utilisation future.¦Le diabète est une maladie caractérisée par un taux élevé de glucose dans le sang (hyperglycémie), résultant d'une incapacité de notre corps à utiliser ou à produire suffisamment d'insuline. A long terme, cette hyperglycémie entraîne une détérioration du système cardio-vasculaire ainsi que de nombreuses complications. On distingue principalement deux type de diabète : le diabète de type 1 et le diabète de type 2, le plus fréquent (environ 90% des cas). Bien que ces deux maladies diffèrent sur beaucoup de points, elles partagent quelques similitudes. D'une part, on décèle une diminution de la quantité de cellules bêta. Cette diminution est cependant partielle dans le cas d'un diabète de type 2, et totale dans celui d'un diabète de type 1. D'autre part, la présence dans la circulation de médiateurs de l'inflammation nommés cytokines est décelée aussi bien chez les patients de type 1 que de type 2. Les cytokines sont sécrétées lors d'une inflammation. Elles servent de moyen de communication entre les différents acteurs de l'inflammation et ont pour certaines un effet néfaste sur la survie des cellules bêta.¦L'objectif principal de ma thèse a été d'étudier en détail l'effet de petites molécules régulatrices de l'expression génique, appelées microARNs. Basé sur le fait que de nombreuses publications ont démontré que les microARNs étaient impliqués dans différentes maladies telles que le cancer, j'ai émis l'hypothèse qu'ils pouvaient également jouer un rôle important dans le développement du diabète.¦Nous avons commencé par mettre des cellules bêta en culture en présence de cytokines, imitant ainsi un environnement inflammatoire. Nous avons pu de ce fait identifier les microARNs dont les niveaux d'expression étaient modifiés. A l'aide de méthodes biochimiques, nous avons ensuite observé que la modulation de certains microARNs par les cytokines avaient des effets néfastes sur la cellule bêta : sur sa production et sa sécrétion d'insuline, ainsi que sur sa mort (apoptose). Nous avons en conséquence pu démontrer que ces petites molécules avaient un rôle important à jouer dans le dysfonctionnement des cellules bêta induit par les cytokines, aboutissant au développement du diabète.¦-¦La cellule bêta pancréatique est une cellule endocrine présente dans les îlots de Langerhans, dans le pancréas. L'insuline, une hormone sécrétée par ces cellules, joue un rôle essentiel dans la régulation de la glycémie. Le diabète se développe si le taux d'insuline relâché par les cellules bêta n'est pas suffisant pour couvrir les besoins métaboliques corporels. Le diabète de type 1, qui représente environ 5 à 10% des cas, est une maladie auto-immune qui se caractérise par une réaction inflammatoire déclenchée par notre système immunitaire envers les cellules bêta. La conséquence de cette attaque est une disparition progressive des cellules bêta. Le diabète de type 2 est, quant à lui, largement plus répandu puisqu'il représente environ 90% des cas. Des facteurs à la fois génétiques et environnementaux sont responsables d'une diminution de la sensibilité des tissus métabolisant l'insuline, ainsi que d'une réduction de la sécrétion de l'insuline par les cellules bêta, ce qui a pour conséquence le développement de la maladie. Malgré les différences entre ces deux types de diabète, ils ont pour points communs la présence d'infiltrat immunitaire et la diminution de l'état fonctionnel des cellules bêta.¦Une meilleure compréhension des mécanismes aboutissant à l'altération de la cellule bêta est primordiale, avant de pouvoir développer de nouvelles stratégies thérapeutiques capables de guérir cette maladie. Durant ma thèse, j'ai donc étudié l'implication de petites molécules d'ARN, régulatrices de l'expression génique, appelées microARNs, dans les conditions physiopathologiques qui aboutissent au développement du diabète. J'ai débuté mon étude par l'identification de microARNs dont le niveau d'expression était modifié lorsque les cellules bêta étaient exposées à des conditions favorisant à la fois le développement du diabète de type 1 (cytokines) et celui du diabète de type 2 (palmitate). Nous avons découvert qu'une modification de l'expression des miR-21, -34a et -146a était commune aux deux traitements. Ces changements d'expressions ont également été confirmés dans deux modèles animaux : les souris NOD qui développent un diabète s'apparentant au diabète de type 1 et les souris db/db qui développent plutôt un diabète de type 2. Puis, à l'aide de puces à ADN, nous avons comparé l'expression de microARNs chez des souris NOD pré-diabétiques. Nous avons alors retrouvé des changements au niveau de l'expression des mêmes microARNs mais également au niveau d'une famille de microARNs : les miR-29a, -29b et -29c. De manière artificielle, nous avons ensuite surexprimé ou inhibé en conditions physiopathologiques l'expression de tous ces microARNs et nous nous sommes intéressés à l'impact d'un tel changement sur différentes fonctions de la cellule bêta comme la synthèse et la sécrétion d'insulinè ainsi que leur survie. Nous avons ainsi pu démontrer que les miR-21, -34a, -29a, -29b, -29c avaient un effet délétère sur la sécrétion d'insuline et que la surexpression de tous ces microARNs (excepté le miR-21) favorisait la mort. Finalement, nous avons démontré que la plupart de ces microARNs étaient impliqués dans la régulation d'importantes voies de signalisation responsables de l'apoptose des cellules bêta telles que les voies de NFKB, BCL2 ou encore JNK.¦Par conséquent, nos résultats démontrent que les microARNs ont un rôle important à jouer dans le dysfonctionnement des cellules bêta lors de la mise en place du diabète.

Potentiel des liposomes pour l'injection intravitréenne de molécules thérapeutiques [Potential of liposomes for the intravitreal injection of therapeutic molecules].

Intravitreal administration has been widely used since 20 years and has been shown to improve the treatment of diseases of the posterior segment of the eye with infectious origin or in edematous maculopathies. This route of administration allows to achieve high concentration of drug in the vitreous and avoids the problems resulting from systemic administration. However, two basic problems limit the use of intravitreal therapy. Many drugs are rapidly cleared from the vitreous humor; therefore, to reach and to maintain effective therapy repeated injections are necessary. Repeated intravitreal injections increase the risk of endophthalmitis, damage to lens, retinal detachment. Moreover, some drugs provoke a local toxicity at their effective dose inducing side-effects and possible retinal lesions. In this context, the development and the use of new drug delivery systems for intravitreal administration are necessary to treat chronic ocular diseases. Among them, particulate systems such as liposomes have been widely studied. Liposomes are easily injectable and permit to reduce the toxicity and to increase the residence time of several drugs in the eye. They are also able to protect in vivo poorly-stable molecules from degradation such as peptides and nucleic acids. Some promising results have been obtained for the treatment of retinitis induced by cytomegalovirus in human and more recently for the treatment of uveitis in animal. Finally, the fate of liposomes in ocular tissues and fluids after their injection into the vitreous and their elimination routes begin to be more known.

Direct binding of peptides to MHC class I molecules on living cells. Analysis at the single cell level.

To directly assess the binding of exogenous peptides to cell surface-associated MHC class I molecules at the single cell level, we examined the possibility of combining the use of biotinylated peptide derivatives with an immunofluorescence detection system based on flow cytometry. Various biotinylated derivatives of the adenovirus 5 early region 1A peptide 234-243, an antigenic peptide recognized by CTL in the context of H-2Db, were first screened in functional assays for their ability to bind efficiently to Db molecules on living cells. Suitable peptide derivatives were then tested for their ability to generate positive fluorescence signals upon addition of phycoerythrin-labeled streptavidin to peptide derivative-bearing cells. Strong fluorescent staining of Db-expressing cells was achieved after incubation with a peptide derivative containing a biotin group at the C-terminus. Competition experiments using the unmodified parental peptide as well as unrelated peptides known to bind to Kd, Kb, or Db, respectively, established that binding of the biotinylated peptide to living cells was Db-specific. By using Con A blasts derived from different H-2 congenic mouse strains, it could be shown that the biotinylated peptide bound only to Db among > 20 class I alleles tested. Moreover, binding of the biotinylated peptide to cells expressing the Dbm13 and Dbm14 mutant molecules was drastically reduced compared to Db. Binding of the biotinylated peptide to freshly isolated Db+ cells was readily detectable, allowing direct assessment of the relative amount of peptide bound to distinct lymphocyte subpopulations by three-color flow cytometry. While minor differences between peripheral T and B cells could be documented, thymocytes were found to differ widely in their peptide binding activity. In all cases, these differences correlated positively with the differential expression of Db at the cell surface. Finally, kinetic studies at different temperatures strongly suggested that the biotinylated peptide first associated with Db molecules available constitutively at the cell surface and then with newly arrived Db molecules.

The normal co-ordinate analysis, vibrational spectra and theoretical infrared intensities of some thiocarbonyl halide molecules /

TITLE: The normal co-ordinate analysis, vibrational spectra and theoretical infrared intensities of some thiocarbonyl halides. AUTHOR: J. L. Brema SUPERVISOR: Dr. D. C. Moule NUMBER OF PAGES: 89 ABSTRACT: The vibrational assignment of the five-in-plane fundamental modes of CSClBr has been made on the basis of infrared gas phase and liquid Raman spectral analyses to supplement our earlier vibrational studies. Even though the one out-of-plane fundamental was not observed spectroscopically an attempt has been made to predict its frequency. The vibrational spectra contained impurity bands and the CSClBr assignment was made only after a thorough analysis of the impurities themselves. A normal co-ordinate analysis calculation was performed assuming a Urey-Bradley force field. This calculation yielded the fundamental frequencies in good agreement with those observed after refinement of the originally transferred force constants. The theoretical frequencies are the eigenvalues of the secular equation and the calculation also gave the corresponding eigenvectors in the form of the very important LLj matrix. The [l] matrix is the transfoirmation between internal co-ordinates and normal co-ordinates and it is essential for Franck-Condon calculations on electronically excited molecules and for infrared Integrated band intensity studies. Using a self-consistent molecular orbital calculation termed "complete neglect of differential overlap" (CNDO/2) , theoretical values of equilibrium bond lengths and angleswere calcuted for a series of carbonyl and thlocarbonyl molecules. From these calculations valence force field force constants were also determined but with limited success. With the CNIX)/2 method theoretical dipole moment derivatives with respect to symmetrized internal co-ordinates were calculated and the results should be useful in a correlation with experimentally determined values.

Elliptical orbital studies of H21 and H2 molecules /|nS. K. Gupta. -- 260 St. Catharines, Ont. : [s. n.],

Calculations are performed on the \S <:Jd ground states of d ' + the H and HC) molecules using a basis set of non-integral ~ ~ I elliptical orbitals. Different variational wavefunctions constructed i- for H~ involved one parameter to three par~~eter variation. In order to l"'educe the ntunber of parameters in most commonly 0- used basis orbitals set, the importance of the term (,+~) Y\ over the term ;u 'Where n is a variational pararneter and the value of cr may be given by boundary condition or cusp condition is outlined in Chapters II and III. It is found that the two parameter -+

Requirements for the selective degradation of CD4 receptor molecules by the human immunodeficiency virus type 1 Vpu protein in the endoplasmic reticulum.

BACKGROUND: HIV-1 Vpu targets newly synthesized CD4 receptor for rapid degradation by a process reminiscent of endoplasmic reticulum (ER)-associated protein degradation (ERAD). Vpu is thought to act as an adaptor protein, connecting CD4 to the ubiquitin (Ub)-proteasome degradative system through an interaction with beta-TrCP, a component of the SCFbeta-TrCP E3 Ub ligase complex. RESULTS: Here, we provide direct evidence indicating that Vpu promotes trans-ubiquitination of CD4 through recruitment of SCFbeta-TrCP in human cells. To examine whether Ub conjugation occurs on the cytosolic tail of CD4, we substituted all four Ub acceptor lysine residues for arginines. Replacement of cytosolic lysine residues reduced but did not prevent Vpu-mediated CD4 degradation and ubiquitination, suggesting that Vpu-mediated CD4 degradation is not entirely dependent on the ubiquitination of cytosolic lysines and as such might also involve ubiquitination of other sites. Cell fractionation studies revealed that Vpu enhanced the levels of ubiquitinated forms of CD4 detected in association with not only the ER membrane but also the cytosol. Interestingly, significant amounts of membrane-associated ubiquitinated CD4 appeared to be fully dislocated since they could be recovered following sodium carbonate salt treatment. Finally, expression of a transdominant negative mutant of the AAA ATPase Cdc48/p97 involved in the extraction of ERAD substrates from the ER membrane inhibited Vpu-mediated CD4 degradation. CONCLUSION: Taken together, these results are consistent with a model whereby HIV-1 Vpu targets CD4 for degradation by an ERAD-like process involving most likely poly-ubiquitination of the CD4 cytosolic tail by SCFbeta-TrCP prior to dislocation of receptor molecules across the ER membrane by a process that depends on the AAA ATPase Cdc48/p97.

Molecules and mechanisms of glial and synaptic plasticity

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

New insights into small molecules inhibitors and protein-protein interactions of VirB8 : a critical conserved component of the type IV secretion system.

Les systèmes bactériens de sécrétion de type IV (T4SS) sont constitués d’un ensemble de 8 à 12 protéines conservées. Ces dernières sont utilisées lors de la translocation de protéines, la translocation de complexes ADN-protéines mais aussi pour le transport de ces derniers au travers de la membrane cellulaire. Les T4SS, en tant que facteurs de virulence pour beaucoup de pathogènes comme Brucella suis, sont donc d’excellents modèles cibles pour le développement de médicaments d’antivirulence. Ces médicaments, en privant le pathogène de son facteur essentiel de virulence : le T4SS, constituent une alternative ou encore une amélioration des traitements antibiotiques utilisés actuellement. VirB8, un facteur d’assemblage conservé dans le T4SS, forme des dimères qui sont importants pour la fonction des T4SS dans ces pathogènes. De par ses interactions multiples, VirB8 est un excellent modèle pour l’analyse des facteurs d’assemblage mais aussi en tant que cible de médicaments qui empêcheraient son interaction avec d’autres protéines et qui, in fine, désarmeraient les bactéries en les privant de leur fonctions essentielles de virulence. À ce jour, nous savons qu’il existe un équilibre monomère-dimère et un processus d’homodimerization de VirB8 dont l’importance est vitale pour la fonctionnement biologique des T4SSs. En se basant sur des essais quantitatifs d’interaction, nous avons identifié (i) des sites potentiels d’interaction avec d’autres protéines VirB du T4SS mais aussi (ii) isolé des petites molécules inhibitrices afin de tester la fonction protéique de VirB8. Afin de déterminer les acides aminés importants pour l’hétérodimérization de VirB8 avec VirB10, nous avons effectué des expériences de mutagenèse aléatoire, de phage display et d’arrimage moléculaire in silico. Ces expériences ont démontré l’importance de trois acides aminés localisés sur le feuillet β : R160, S162, T164 et I165. Ces derniers seraient importants pour l’association de VirB8 avec VirB10 étant donné que leur mutagenèse entraine une diminution de la formation du complexe VirB8-VirB10. L’objectif actuel de notre projet de recherche est de pouvoir mieux comprendre mais aussi d’évaluer le rôle de VirB8 dans l’assemblage du T4SS. Grace à un méthode de criblage adaptée à partir de la structure de VirB8, nous avons pu identifié une petite molécule inhibitrice BAR-068, qui aurait un rôle prometteur dans l’inhibition du T4SS. Nous avons utilisé la spectroscopie par fluorescence, l’essai à deux hybrides, le cross-linking et la cristallographie afin de déterminer le mécanisme d'interaction existant entre VirB8 et BAR-068. Ces travaux pourraient permettre de nombreuses avancées, notamment en termes de compréhension des mécanismes d’inhibition du T4SS. Notre objectif ultime est de pouvoir caractériser la séquence d’évènements essentiels à l’assemblage et au fonctionnement du T4SS. De manière globale, notre projet de recherche permettrait de révéler les grands principes d’assemblage des protéines membranaires, les processus de sécrétion de protéines chez les bactéries mais aussi de proposer une nouvelle stratégie lors du développement de drogues antimicrobiennes.

Photothermal Investigations on certain Organic Molecules and their Plasma polymerized thin Films

Department of Physics, Cochin University of Science and Technology

Photothermal Investigations on Certain Plasma Polymerized Thin Films and Near IR Overtone Studies of Some Organic Molecules

Photothermal effect refers to heating of a sample due to the absorption of electromagnetic radiation. Photothermal (PT) heat generation which is an example of energy conversion has in general three kinds of applications. 1. PT material probing 2. PT material processing and 3. PT material destruction. The temperatures involved increases from 1-. 3. Of the above three, PT material probing is the most important in making significant contribution to the field of science and technology. Photothermal material characterization relies on high sensitivity detection techniques to monitor the effects caused by PT material heating of a sample. Photothermal method is a powerful high sensitivity non-contact tool used for non-destructive thermal characterization of materials. The high sensitivity of the photothermal methods has led to its application for analysis of low absorbance samples. Laser calorimetry, photothermal radiometry, pyroelectric technique, photoacoustic technique, photothermal beam deflection technique, etc. come under the broad class ofphotothermal techniques. However the choice of a suitable technique depends upon the nature of the sample, purpose of measurement, nature of light source used, etc. The present investigations are done on polymer thin films employing photothermal beam deflection technique, for the successful determination of their thermal diffusivity. Here the sample is excited by a He-Ne laser (A = 6328...\ ) which acts as the pump beam. Due to the refractive index gradient established in the sample surface and in the adjacent coupling medium, another optical beam called probe beam (diode laser, A= 6500A ) when passed through this region experiences a deflection and is detected using a position sensitive detector and its output is fed to a lock-in amplifier from which the amplitude and phase of the deflection can be directly obtained. The amplitude and phase of the signal is suitably analysed for determining the thermal diffusivity.The production of polymer thin film samples has gained considerable attention for the past few years. Plasma polymerization is an inexpensive tool for fabricating organic thin films. It refers to formation of polymeric materials under the influence of plasma, which is generated by some kind of electric discharge. Here plasma of the monomer vapour is generated by employing radio frequency (MHz) techniques. Plasma polymerization technique results in homogeneous, highly adhesive, thermally stable, pinhole free, dielectric, highly branched and cross-linked polymer films. The possible linkage in the formation of the polymers is suggested by comparing the FTIR spectra of the monomer and the polymer.Near IR overtone investigations on some organic molecules using local mode model are also done. Higher vibrational overtones often provide spectral simplification and greater resolution of peaks corresponding to nonequivalent X-H bonds where X is typically C, N or O. Vibrational overtone spectroscopy of molecules containing X-H oscillators is now a well established tool for molecular investigations. Conformational and steric differences between bonds and structural inequivalence ofCH bonds (methyl, aryl, acetylenic, etc.) are resolvable in the higher overtone spectra. The local mode model in which the X-H oscillators are considered to be loosely coupled anharmonic oscillators has been widely used for the interpretation of overtone spectra. If we are exciting a single local oscillator from the vibrational ground state to the vibrational state v, then the transition energy of the local mode overtone is given by .:lE a......v = A v + B v2 • A plot of .:lE / v versus v will yield A, the local mode frequency as the intercept and B, the local mode diagonal anharmonicity as the slope. Here A - B gives the mechanical frequency XI of the oscillator and B = X2 is the anharmonicity of the bond. The local mode parameters XI and X2 vary for non-equivalent X-H bonds and are sensitive to the inter and intra molecular environment of the X-H oscillator.

Twin peak distribution of electron emission profile and impact ionization of ambient molecules during laser ablation of silver target

Laser-induced plasma generated from a silver target under partial vacuum conditions using the fundamental output of nanosecond duration from a pulsed Nd:yttrium aluminum garnet laser is studied using a Langmuir probe. The time of flight measurements show a clear twin peak distribution in the temporal profile of electron emission. The first peak has almost the same duration as the laser pulse while the second lasts for several microseconds. The prompt electrons are energetic enough ('60 eV) to ionize the ambient gas molecules or atoms. The use of prompt electron pulses as sources for electron impact excitation is demonstrated by taking nitrogen, carbon dioxide, and argon as ambient gases.

Spectral studies of naphthalocyanine (Nc) and rare earth phthalocyanine (RePc) molecules in an inorganic glassy borate matrix

Optical absorption and emission spectral studies of free and metal naphthalocyanine doped borate glass matrix are reported for the first time. Absorption spectra recorded in the UV- VIS-NIR region show the characteristic absorption bands, namely, the B-band and Q-band of the naphthalocyanine (Nc) molecule. Some of the important spectral parameters, namely, the optical absorption coefficient (α), molar extinction coefficient (ε) and absorption cross section (σa) of the principal absorption transitions are determined. Optical band gap (Eg) of the materials evaluated from the functional dependence of absorption coefficient on photon energy lies in the range 1.6 eV≤Eg≤2.1 eV. All fluorescence spectra except that of EuNc consist of an intense band in the 765 nm region corresponding to the excitation of Q-band. In EuNc the maximum fluorescence intensity band is observed at 824 nm. The intensity of the principal fluorescence band is maximum in ZnNc, whereas it is minimum in H2Nc. Radiative parameters of the principal fluorescence transitions corresponding to the Q-band excitation are also reported for the naphthalocyanine and phthalocyanine based matrices.