The role of frameshifting and transcriptional dysregulation in spinocerebellar ataxia type-3

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Metabolic signatures of Huntington's disease (HD): 1H NMR analysis of the polar metabolome in post mortem human brain

Huntington’s disease (HD) is an autosomal neurodegenerative disorder affecting approximately 5-10 persons per 100,000 worldwide. The pathophysiology of HD is not fully understood but the age of onset is known to be highly dependent on the number of CAG triplet repeats in the huntingtin gene. Using 1H NMR spectroscopy this study biochemically profiled 39 brain metabolites in post-mortem striatum (n=14) and frontal lobe (n=14) from HD sufferers and controls (n=28). Striatum metabolites were more perturbed with 15 significantly affected in HD cases, compared with only 4 in frontal lobe (P<0.05; q<0.3). The metabolite which changed most overall was urea which decreased 3.25-fold in striatum (P<0.01). Four metabolites were consistently affected in both brain regions. These included the neurotransmitter precursors tyrosine and L-phenylalanine which were significantly depleted by 1.55-1.58-fold and 1.48-1.54-fold in striatum and frontal lobe, respectively (P=0.02-0.03). They also included L-leucine which was reduced 1.54-1.69-fold (P=0.04-0.09) and myo-inositol which was increased 1.26-1.37-fold (P<0.01). Logistic regression analyses performed with MetaboAnalyst demonstrated that data obtained from striatum produced models which were profoundly more sensitive and specific than those produced from frontal lobe. The brain metabolite changes uncovered in this first 1H NMR investigation of human HD offer new insights into the disease pathophysiology. Further investigations of striatal metabolite disturbances are clearly warranted.

Spectroscopy and metastability of CO 2 2+ molecular ions

The spectroscopy and metastability of the carbon dioxide doubly charged ion, the CO ₂ ²⁺ dication, have been studied with photoionization experiments: time-of-flight photoelectron photoelectron coincidence (TOF-PEPECO), threshold photoelectrons coincidence (TPEsCO), and threshold photoelectrons and ion coincidence (TPEsCO ion coincidence) spectroscopies. Vibrational structure is observed in TOF-PEPECO and TPEsCO spectra of the ground and first two excited states. The vibrational structure is dominated by the symmetric stretch except in the TPEsCO spectrum of the ground state where an antisymmetric stretch progression is observed. All three vibrational frequencies are deduced for the ground state and symmetric stretch and bending frequencies are deduced for the first two excited states. Some vibrational structure of higher electronic states is also observed. The threshold for double ionization of carbon dioxide is reported as 37.340±0.010 eV. The fragmentation of energy selected CO ₂ ²⁺ ions has been investigated with TPEsCO ion coincidence spectroscopy. A band of metastable states from ∼38.7 to ∼41 eV above the ground state of neutral CO ₂ has been observed in the experimental time window of ∼0.1-2.3 μs with a tendency towards shorter lifetimes at higher energies. It is proposed that the metastability is due to slow spin forbidden conversion from bound excited singlet states to unbound continuum states of the triplet ground state. Another result of this investigation is the observation of CO ⁺+O ⁺ formation in indirect dissociative double photoionization below the threshold for formation of CO ₂ ²⁺. The threshold for CO ⁺+O ⁺ formation is found to be 35.56±0.10 eV or lower, which is more than 2 eV lower than previous measurements.

Towards NIR emission: 2-(1H-tetrazol-1-yl)pyridine as versatile ligand for the synthesis of two new families of cationic and neutral Ir(III) complexes.

In the last decades, cyclometalated Ir(III) complexes have drawn a large interest for their unique properties: they are excellent triplet state emitters, thus the emission is phosphorescent in nature; typically high quantum yields and good stability make them good candidates for luminescent materials. Moreover, through an opportune choice of the ligands, it is possible to tune the emission along the whole visible spectra. Thanks to these interesting features, Ir(III) complexes have found different applications in several areas of applied science, from OLEDs to bioimaging. In particular, regarding the second application, a remarkable red-shift in the emission is required, in order to minimize the problem of the tissue penetration and the possible damages for the organisms. With the aim of synthesizing a new family of NIR emitting Ir(III) complexes, we envisaged the possibility to use for the first time 2-(1H-tetrazol-1-yl)pyridine as bidentate ligand able to provide the required red-shift of the emission of the final complexes. Exploiting the versatility of the ligand, I prepared two different families of heteroleptic Ir(III) complexes. In detail, in the first case the 2-(1H-tetrazol-1-yl)pyridine was used as bis-chelating N^N ligand, leading to cationic complexes, while in the second case it was used as cyclometalating C^N ligand, giving neutral complexes. The structures of the prepared molecules have been characterised by NMR spectroscopy and mass spectrometry. Moreover, the neutral complexes’ emissive properties have been measured: emission spectra have been recorded in solution at both room temperature and 77K, as well as in PMMA matrix. DFT calculation has then been performed and the obtained results have been compared to experimental ones.

Mixing of 0(+) and 0(-) observed in the hyperfine and Zeeman structure of ultracold Rb-2 molecules

We study the combination of the hyperfine and Zeeman structure in the spin-orbit coupled A(1)Sigma(+)(u) = b(3)Pi(u) complex of Rb-87(2). For this purpose, absorption spectroscopy at a magnetic field around B = 1000 G is carried out. We drive optical dipole transitions from the lowest rotational state of an ultracold Feshbach molecule to various vibrational levels with 0(+) symmetry of the A - b complex. In contrast to previous measurements with rotationally excited alkali-dimers, we do not observe equal spacings of the hyperfine levels. In addition, the spectra vary substantially for different vibrational quantum numbers, and exhibit large splittings of up to 160 MHz, unexpected for 0(+) states. The level structure is explained to be a result of the repulsion between the states 0(+) and 0(-) of b(3)Pi(u), coupled via hyperfine and Zeeman interactions. In general, 0(-) and 0(+) have a spin-orbit induced energy spacing Delta, that is different for the individual vibrational states. From each measured spectrum we are able to extract Delta, which otherwise is not easily accessible in conventional spectroscopy schemes. We obtain values of Delta in the range of +/- 100 GHz which can be described by coupled channel calculations if a spin-orbit coupling is introduced that is different for 0(-) and 0(+) of b(3)Pi(u).

Universality of weakly bound dimers and Efimov trimers close to Li-Cs Feshbach resonances

We study the interspecies scattering properties of ultracold Li-Cs mixtures in their two energetically lowest spin channels in the magnetic field range between 800 and 1000 G. Close to two broad Feshbach resonances (FR) we create weakly bound LiCs dimers by radio-frequency association and measure the dependence of their binding energy on the external magnetic field strength. Based on the binding energies and complementary atom loss spectroscopy of three other Li-Cs s-wave FRs we construct precise molecular singlet and triplet electronic ground state potentials using a coupled-channels calculation. We extract the Li-Cs interspecies scattering length as a function of the external field and obtain almost a ten-fold improvement in the precision of the values for the pole positions and widths of the s-wave FRs as compared to our previous work (Pires et al 2014 Phys. Rev. Lett. 112 250404). We discuss implications on the Efimov scenario and the universal geometric scaling for LiCsCs trimers.

Zbadanie prądu tunelowego w złączach typu metal-nadprzewodnik trypletowy dla wybranych symetrii parametru porządku

Wydział Fizyki: Zakład Teorii Ciała Stałego

Friedreich Ataxia

Friedreich's ataxia (FRDA) is the most common autosomal recessive hereditary ataxia in Caucasians. Neurological symptoms dominate the clinical picture. The underlying neuropathology affects the dorsal root ganglia, the spinal cord, and the deep cerebellar nuclei. In addition, most cases present a hypertrophic cardiomyopathy that may cause premature death. Other problems include a high risk of diabetes, skeletal abnormalities such as kyphoscoliosis, and pes cavus. Most patients carry a homozygous expansion of GAA trinucleotide repeat within the first intron of the FXN gene, leading to repressed transcription through epigenetic mechanisms. The encoded protein, frataxin, is localized in mitochondria and participates in the biogenesis of iron-sulfur clusters. Frataxin deficiency leads to mitochondrial dysfunction, altered iron metabolism, and oxidative damage. Thanks to progress in understanding pathogenesis and to the development of animal and cellular models, therapies targeted to correct frataxin deficiency or its downstream consequences are being developed and tested in clinical trials.

Friedreich Ataxia

Friedreich ataxia (FRDA) is an autosomal recessive disease characterized by progressive neurological and cardiac abnormalities. It has a prevalence of around 2×10⁵ in whites, accounting for more than one-third of the cases of recessively inherited ataxia in this ethnic group. FRDA may not exist in nonwhite populations.The first symptoms usually appear in childhood, but age of onset may vary from infancy to adulthood. Atrophy of sensory and cerebellar pathways causes ataxia, dysarthria, fixation instability, deep sensory loss, and loss of tendon reflexes. Corticospinal degeneration leads to muscular weakness and extensor plantar responses. A hypertrophic cardiomyopathy may contribute to disability and cause premature death. Other common problems include kyphoscoliosis, pes cavus, and, in 10% of patients, diabetes mellitus.The FRDA gene (FXN) encodes a small mitochondrial protein, frataxin, which is produced in insufficient amounts in the disease, as a consequence of the epigenetic silencing of the gene triggered by a GAA triplet repeat expansion in the first intron of the gene. Frataxin deficiency results in impaired iron-sulfur cluster biogenesis in mitochondria, in turn leading to widespread dysfunction of iron-sulfur center containing enzymes (in particular respiratory complexes I, II and III, and aconitase), impaired iron metabolism, oxidative stress, and mitochondrial dysfunction. Therapy aims to restore frataxin levels or to correct the consequences of its deficiency.

Theoretical Rationalization of the Singlet–Triplet Gap in OLEDs Materials: Impact of Charge-Transfer Character

New materials for OLED applications with low singlet–triplet energy splitting have been recently synthesized in order to allow for the conversion of triplet into singlet excitons (emitting light) via a Thermally Activated Delayed Fluorescence (TADF) process, which involves excited-states with a non-negligible amount of Charge-Transfer (CT). The accurate modeling of these states with Time-Dependent Density Functional Theory (TD-DFT), the most used method so far because of the favorable trade-off between accuracy and computational cost, is however particularly challenging. We carefully address this issue here by considering materials with small (high) singlet–triplet gap acting as emitter (host) in OLEDs and by comparing the accuracy of TD-DFT and the corresponding Tamm-Dancoff Approximation (TDA), which is found to greatly reduce error bars with respect to experiments thanks to better estimates for the lowest singlet–triplet transition. Finally, we quantitatively correlate the singlet–triplet splitting values with the extent of CT, using for it a simple metric extracted from calculations with double-hybrid functionals, that might be applied in further molecular engineering studies.

Surface photochemistry: photodegradation study of pyrene adsorbed onto microcrystalline cellulose and silica

Ground-state diffuse reflectance, time resolved laser-induced luminescence, diffuse reflectance laser flash-photolysis transient absorption and chromatographic techniques were used to elucidate the photodegradation processes of pyrene adsorbed onto microcrystalline cellulose and silica. Ground-state diffuse reflectance showed that on both substrates low concentrations display absorption of pyrene monomers. At high concentrations spectral changes attributed to aggregate formation were observed. Laser induced fluorescence showed that pyrene onto microcrystalline cellulose mainly presents fluorescence from monomers, while for silica, excimer-like emission was observed from low surface loadings (greater than or equal to 0.5 mumol g(-1)). Transient absorption and photodegradation studies were performed at concentrations where mainly monomers exist. On silica, pyrene presents transient absorption from its radical cation. On microcrystalline cellulose both radical cation, radical anion and pyrene triplet-triplet absorption were detected. Irradiation followed by chromatographic analysis showed that pyrene decomposes on both substrates. For pyrene on microcrystalline cellulose 1-hydroxypyrene was the main identified photoproduct since in the absence of oxygen further oxidation of 1-hydroxypyrene was very slow. For pyrene on silica photodegradation was very efficient. Almost no 1-hydroxypyrene was detected since in the presence of oxygen it is quickly oxidized to other photooxidation products. On both substrates, pyrene radical cation is the intermediate leading to photoproducts and oxygen it is not involved in its formation.

A diffuse reflectance comparative study of benzil inclusion within microcrystalline cellulose and beta-cyclodextrin

Diffuse reflectance and laser-induced techniques were used to study photochemical and photophysical processes of benzil adsorbed on two solid powdered supports, microcrystalline cellulose and beta-cyclodextrin. In both substrates, a distribution of ground-state benzil conformers exists, largely dominated by skew conformations where the carbonyl groups are twisted one to the other. Room temperature phosphorescence was observed in air-equilibrated samples in both cases. The decay times vary greatly and the largest lifetime was obtained for benzil/beta-cyclodextrin, showing that this host's cavity accommodates benzil well, enhancing its room temperature phosphorescence. Triplet - triplet absorption of benzil entrapped in cellulose was detected and benzil ketyl radical formation also occurred. With benzil included into beta-cyclodextrin, and following laser excitation, benzoyl radicals were detected on the millisecond timescale. Product analysis and identification of laser-irradiated benzil samples in the two hosts clearly showed that the main degradation photoproducts were benzoic acid and benzaldehyde. The main differences were a larger benzoic acid/benzaldehyde ratio in the case of cellulose and the formation of benzyl alcohol in this support.

Novel laser-induced luminescence resulting from benzophenone/O-propylated p-tert-butylcalix[4]arene complexes. A diffuse reflectance study

Laser-induced room temperature luminescence of air-equilibrated benzophenone/O-propylated p-tert-butylcalix[ 4] arene solid powdered samples revealed the existence of a novel emission, in contrast with benzophenone/p-tertbutylcalix[ 4] arene complexes, where only benzophenone emits. This novel emission was identified as phosphorescence of 1-phenyl-1,2-propanedione, which is formed as the result of an hydrogen atom abstraction reaction of the triplet excited benzophenone from the propoxy substituents of the calixarene. Room temperature phosphorescence was obtained in air-equilibrated samples in all propylated hosts. The decay times of the benzophenone emission vary greatly with the degree of propylation, the shortest lifetimes being obtained in the tri- and tetrapropylated calixarenes. Triplet - triplet absorption of benzophenone was detected in all cases, and is the predominant absorption in the p-tert-butylcalix[ 4] arene case, where an endo-calix complex is formed. Benzophenone ketyl radical formation occurs with the O-propylated p-tert-butylcalix[ 4] arenes hosts, suggesting a different type of host/guest molecular arrangement. Diffuse reflectance laser. ash photolysis and gas chromatography - mass spectrometry techniques provided complementary information, the former about transient species and the latter regarding the final products formed after light absorption. Product analysis and identification clearly show that the two main degradation photoproducts following laser excitation in the propylated substrates are 1-phenyl-1,2- propanedione and 2- hydroxybenzophenone, although several other minor photodegradation products were identified. A detailed mechanistic analysis is proposed. While the solution photochemistry of benzophenone is dominated by the hydrogen abstraction reaction from suitable hydrogen donors, in these solid powdered samples, the alpha-cleavage reaction also plays an important role. This finding occurs even with one single laser pulse which lasts only a few nanoseconds, and is apparently related to the fact that scattered radiation exists, due to multiple internal reflections possibly trapping light within non-absorbing microcrystals in the sample, and is detected until at least 20 mus after the laser pulse. This could explain how photoproducts thus formed could also be excited with only one laser pulse.

A diffuse reflectance comparative study of benzil inclusion within p-tert-butylcalix[n]arenes (n=4, 6, and 8) and silicalite

Diffuse reflectance and laser-induced techniques were used to access photochemical and photophysical processes of benzil in solid supports, namely p-tert-butylcalix[n]arenes with n = 4, 6, and 8. A comparative study was performed using these results and those obtained with another electronically inert support, silicalite, which is a hydrophobic zeolite. In the latter substrate, ground-state benzil has the two carbonyl groups in an s-trans planar conformation while in the calixarenes a distribution of conformers exists, largely dominated by skew conformations where the carbonyl groups are twisted one to the other. In all substrates, room-temperature phosphorescence was obtained in air-equilibrated samples. The decay times vary greatly and the largest lifetime was obtained for benzil/p-tert-butylcalix[6]arene, showing that this host cavity well accommodates benzil, enhancing its room-temperature phosphorescence. p-tert-Butylcalix[6] and [8]arene molecules provide larger hydrophobic cavities than silicalite, and inclusion complexes are formed with these hosts and benzil as guest; p-tert-butylcalix[4]arene does not include benzil. This probe is deposited outside the calix[41 cavity, in the form of microcrystals. Triplet-triplet absorption of benzil was detected in all cases and is predominant in the silicalite channel inclusion case. Benzil ketyl radical formation occurs with inclusion in calix[6]arene and calix[8]arene. In the three cases, benzoyl radical was detected at long times (in the millisecond time scale). Product analysis and identification clearly show that the main detected degradation photoproducts in all substrates are benzoyl radical derivatives. Calix[6] and [8]arenes are able to supply hydrogen atoms that allow also another reaction, the reduction to benzoin through benzil ketyl radical formation.

Transfert ultrarapide d’électron et transfert modéré d’énergie au sein d’assemblages supramoléculaires de colorants et d’un cluster de palladium

Résumé : Les transferts d’électrons photo-induits et d’énergie jouent un rôle primordial dans un grand nombre de processus photochimiques et photobiologiques, comme la respiration ou la photosynthèse. Une très grande quantité de systèmes à liaisons covalentes ont été conçus pour copier ces processus de transferts. Cependant, les progrès sont, en grande partie, limités par les difficultés rencontrées dans la synthèse de nouveaux couples de types donneurs-accepteurs. Récemment, des espèces utilisant des liaisons non-covalentes, comme les liaisons hydrogènes, les interactions [pi]-[pi], les liaisons de coordination métal-ligands ou encore les interactions électrostatiques sont le centre d’un nouvel intérêt du fait qu’ils soient plus faciles à synthétiser et à gérer pour obtenir des comportements de transferts d’électrons ou d’énergie plus flexibles et sélectifs. C’est dans cette optique que le travail de cette thèse a été mené, i.e. de concevoir des composés auto-assemblés avec des porphyrines et un cluster de palladium pour l’étude des transferts d’électrons photo-induits et d’énergie. Cette thèse se divise en quatre parties principales. Dans la première section, le chapitre 3, deux colorants porphyriniques, soit le 5-(4-carboxylphényl)-10, 15, 20-tristolyl(porphyrinato)zinc(II) (MCP, avec Na+ comme contre-ion) et 5, 15-bis(4-carboxylphényl)-15, 20-bistolyl(porphyrinato)zinc(II) (DCP, avec Na+ comme contre-ion) ont été utilisés comme donneurs d’électrons, et le [Pd3(dppm)3(CO)]2+ ([Pd32+], dppm = (Ph2P)2CH2, PF6‾ est le contre-ion) a été choisi comme accepteur d’électrons. La structure de l’assemblage [Pd32+]•••porphyrine a été élucidée par l’optimisation des géométries à l’aide de calculs DFT. La spectroscopie d’absorption transitoire (TAS) montre la vitesse de transferts d’électrons la plus rapide (< 85 fs, temps inférieurs à la limite de détection) jamais enregistrée pour ce type de système (porphyrine-accepteur auto-assemblés). Généralement, ces processus sont de l’ordre de l’échelle de la ps-ns. Cette vitesse est comparable aux plus rapides transferts d’électrons rapportés dans le cas de systèmes covalents de type porphyrine-accepteur rapide (< 85 fs, temps inférieurs à la limite de détection). Ce transfert d’électrons ultra-rapide (ket > 1.2 × 1013 s-1) se produit à l’état énergétique S1 des colorants dans une structure liée directement par des interactions ioniques, ce qui indique qu’il n’est pas nécessaire d’avoir de forts liens ou une géométrie courbée entre le donneur et l’accepteur. Dans une deuxième section, au chapitre 4, nous avons étudié en profondeur l’effet de l’utilisation de porphyrines à systèmes π-étendus sur le comportement des transferts d’électrons. Le colorant 9, 18, 27, 36-tétrakis-meso-(4-carboxyphényl)tétrabenzoporphyrinatozinc(II) (TCPBP, avec Na+ comme contre-ion) a été sélectionné comme candidat, et le 5, 10, 15, 20-tétrakis-meso-(4-carboxyphényl)porphyrineatozinc(II) (TCPP, avec Na+ comme contre-ion) a aussi été utilisé à des fins de comparaisons. TCPBP et TCPP ont, tous deux, été utilisés comme donneurs d’électrons pour fabriquer des assemblages supramoléculaires avec le cluster [Pd32+] comme accepteur d’électrons. Les calculs DFT ont été réalisés pour expliquer les structures de ces assemblages. Dans les conditions expérimentales, ces assemblages sont composés principalement d’une porphyrine avec 4 équivalents de clusters. Ces systèmes ont aussi été investigués par des mesures de quenching (perte de luminescence), par électrochimie et par d’autres techniques. Les transferts d’électrons (< 85 fs; temps inférieurs à la limite de détection) étaient aussi observés, de façon similaire aux assemblages MCP•••[Pd32+] et [Pd32+]•••DCP•••[Pd32+]. Les résultats nous indiquent que la modification de la structure de la porphyrine vers la tétrabenzoporphyrine ne semble pas influencer le comportement des cinétiques de transferts d’électrons (aller ou retour). Dans la troisième section, le chapitre 5, nous avons synthétisé la porphyrine hautement [pi]-conjuguée: 9, 18, 27, 36-tétra-(4-carboxyphényléthynyl)tétrabenzoporphyrinatozinc(II) (TCPEBP, avec Na+ comme contre-ion) par des fonctionnalisations en positions meso- et β, β-, qui présente un déplacement vers le rouge de la bande de Soret et des bandes Q. TCPEBP était utilisé comme donneur d’électrons pour fabriquer des motifs supramoléculaires avec le [Pd32+] comme accepteur d’électrons. Des expériences en parallèle ont été menées en utilisant la 5, 10, 15, 20-tétra-(4-carboxyphényl)éthynylporphyrinatozinc(II) (TCPEP, avec Na+ comme contre-ion). Des calculs DFT et TDDFT ont été réalisés pour de nouveau déterminer de façon théorique les structures de ces systèmes. Les constantes d’association pour les assemblages TCPEBP•••[Pd32+]x sont les plus élevées parmi tous les assemblages entre des porphyrines et le cluster de palladium rencontrés dans la littérature. La TAS a montré, encore une fois, des processus de transferts d’électrons dans des échelles de l’ordre de 75-110 fs. Cependant, les transferts de retour d’électrons sont aussi très rapides (< 1 ps), ce qui est un obstacle potentiel pour des applications en cellules solaires à pigment photosensible (DSSCs). Dans la quatrième section, le chapitre 6, les transferts d’énergie triplets (TET) ont été étudiés pour les assemblages MCP•••[Pd32+] et [Pd32+]•••DCP•••[Pd32+]. Les analyses spectrales des états transitoires dans l’échelle de temps de la ns-[mu]s démontrent de façon évidente les TETs; ceux-ci présentent des transferts d’énergie lents et/ou des vitesses moyennes pour des transferts d’énergie T1-T1 (3dye*•••[Pd32+] → dye•••3[Pd32+]*) opérant à travers exclusivement le mécanisme de Förster avec des valeurs de kET autour de ~ 1 × 105 s-1 selon les mesures d’absorption transitoires à 298 K. Des forces motrices non-favorables rendent ces types de processus non-opérants ou très lents dans les états T1. L’état T1 de [Pd32+] (~8190 cm-1) a été qualitativement déterminé par DFT et par la mise en évidence de l’émission S0 ← Tn retardée à 680-700 nm provenant de l’annihilation T1-T1, ce qui fait que ce cluster peut potentiellement agir comme un donneur à partir de ses états Tn, et accepteur à partir de T1 à l’intérieur de ces assemblages. Des pertes d’intensités de types statiques pour la phosphorescence dans le proche-IR sont observées à 785 nm. Ce travail démontre une efficacité modérée des colorants à base de porphyrines pour être impliquée dans des TETs avec des fragments organométalliques, et ce, même attachées grâce à des interactions ioniques. En conclusion, les assemblages ioniques à base de porphyrines et de clusters de palladium présentent des propriétés de transferts d’électrons S1 ultra-rapides, et des transferts d’énergie T1 de vitesses modérées, ce qui est utile pour de possibles applications comme outils optoélectroniques. D’autres études, plus en profondeur, sont présentement en progrès.