MicroARN (miARN) ont récemment émergé comme un acteur central du gène réseau de régulation impliqués dans la prise du destin cellulaire. L'apoptose, un actif processus, par lequel des cellules déclenchent leur auto-destruction en réponse à un signal, peut être contrôlé par les miARN. Il a également été impliqué dans une variété de maladies humaines, comme les maladies du cœur, et a été pensé comme une cible pour le traitement de la maladie. Tanshinone IIA (TIIA), un monomère de phenanthrenequinones utilisé pour traiter maladies cardiovasculaires, est connu pour exercer des effets cardioprotecteurs de l'infarctus du myocarde en ciblant l'apoptose par le renforcement de Bcl-2 expression. Pour explorer les liens potentiels entre le miARN et l'action anti-apoptotique de TIIA, nous étudié l'implication possible des miARN. Nous avons constaté que l'expression de tous les trois membres de la famille miR-34, miR-34a, miR-34b et miR-34c ont été fortement régulée à la hausse après l'exposition soit à la doxorubicine, un agent endommageant l'ADN ou de pro-oxydant H2O2 pendant 24 heures. Cette régulation à la hausse causé significativement la mort cellulaire par apoptose, comme déterminé par fragmentation de l'ADN, et les effets ont été renversés par les ARNs antisens de ces miARN. Le prétraitement des cellules avec TIIA avant l'incubation avec la doxorubicine ou H2O2 a empêché surexpression de miR-34 et a réduit des apoptose. Nous avons ensuite établi BCL2L2, API5 et TCL1, en plus de BCL2, comme les gènes nouveaux cibles pour miR-34. Nous avons également élucidé que la répression des ces gènes par MiR-34 explique l'effet proapoptotique dans les cardiomyocytes. Ce que la régulation positive de ces gènes par TIIA realisée par la répression de l'expression de miR-34 est probable le mécanisme moléculaire de son effet bénéfique contre ischémique lésions cardiaques. / MiRNAs (miRNAs) have recently emerged as a central player of gene regulatory network involved in decision of cell fate. Apoptosis, an active process that leads to cell death, has been shown to be controlled by miRNAs. It has also been implicated in a variety of human disease, such as heart disease, and established as a target process for disease therapy. Tanshinone IIA (TIIA), a monomer of phenanthrenequinones used to treat cardiovascular diseases, is known to exert cardioprotective effects in myocardial infarction by targeting apoptosis through enhancing Bcl-2 expression. To explore the potential link between miRNAs and the anti-apoptotic action of TIIA, we studied the possible involvement of miRNAs. We found that expression of all three members of the miR-34 family, miR-34a, miR-34b and miR-34c that have been known to mediate the apoptotic effect of p53 in cancer cells, were robustly upregulated after exposure to either the DNA-damaging agent doxorubicin or pro-oxidant H2O2 for 24 hr in cultured neonatal rat ventricular myocytes. This upregulation caused significant apoptotic cell death, as determined by DNA fragmentation, and the effects were reversed by the antisense to these miRNAs. Pretreatment of cells with TIIA prior to incubation with doxorubicin or H2O2 prevented upregulation of miR-34 and reduced apoptosis. We then established BCL2L2, API5 and TCL1, in addition to BCL2, as the novel target genes for miR-34. We further unraveled that repression of these genes by miR-34 accounts for its proapoptotic effect in cardiomyocytes whereas upregulation of these genes by TIIA through downregulating miR-34 is likely the molecular mechanism for its beneficial effect against ischemic myocardial injuries.

La fibrillation auriculaire (FA) est le trouble du rythme le plus fréquemment observé en pratique clinique. Elle constitue un risque important de morbi-mortalité. Le traitement de la FA reste un défi majeur en lien avec les nombreux effets secondaires associés aux approches thérapeutiques actuelles. Dans ce contexte, une meilleure compréhension des mécanismes sous-jacents à la FA est essentielle pour le développement de nouvelles thérapies offrant un meilleur rapport bénéfice/risque pour les patients. La FA est caractérisée par i) un remodelage électrique délétère associé le plus souvent ii) à un remodelage structurel du myocarde favorisant la récurrence et le maintien de l’arythmie. La diminution de la période réfractaire effective au sein du tissu auriculaire est un élément clef du remodelage électrique. Le remodelage structurel, quant à lui, se manifeste principalement par une fibrose tissulaire qui altère la propagation de l’influx électrique dans les oreillettes. Les mécanismes moléculaires impliqués dans la mise en place de ces deux substrats restent mal connus. Récemment, le rôle des microARNs (miARNs) a été pointé du doigt dans de nombreuses pathologies notamment cardiaques. Dans ce contexte les objectifs principaux de ce travail ont été i) d'acquérir une compréhension approfondie du rôle des miARNs dans la régulation de l’expression des canaux ioniques et ii) de mieux comprendre le rôle de ces molécules dans l’installation d’un substrat favorable a la FA. Nous avons, dans un premier temps, effectué une analyse bio-informatique combinée à des approches expérimentales spécifiques afin d’identifier clairement les miARNs démontrant un fort potentiel de régulation des gènes codant pour l’expression des canaux ioniques cardiaques humains. Nous avons identifié un nombre limité de miARNs cardiaques qui possédaient ces propriétés. Sur la base de ces résultats, nous avons démontré que l’altération de l'expression des canaux ioniques, observée dans diverse maladies cardiaques (par exemple, les cardiomyopathies, l’ischémie myocardique, et la fibrillation auriculaire), peut être soumise à ces miARNs suggérant leur implication dans l’arythmogénèse. La régulation du courant potassique IK1 est un facteur déterminant du remodelage électrique auriculaire associée à la FA. Les mécanismes moléculaires sous-jacents sont peu connus. Nous avons émis l’hypothèse que l'altération de l’expression des miARNs soit corrélée à l’augmentation de l’expression d’IK1 dans la FA. Nous avons constaté que l’expression de miR-26 est réduite dans la FA et qu’elle régule IK1 en modulant l’expression de sa sous-unité Kir2.1. Nous avons démontré que miR-26 est sous la répression transcriptionnelle du facteur nucléaire des lymphocytes T activés (NFAT) et que l’activité accrue de NFATc3/c4, aboutit à une expression réduite de miR-26. En conséquence IK1 augmente lors de la FA. Nous avons enfin démontré que l’interférence in vivo de miR-26 influence la susceptibilité à la FA en régulant IK1, confirmant le rôle prépondérant de miR-26 dans le remodelage auriculaire électrique. La fibrose auriculaire est un constituant majeur du remodelage structurel associé à la FA, impliquant l'activation des fibroblastes et l’influx cellulaire du Ca2 +. Nous avons cherché à déterminer i) si le canal perméable au Ca2+, TRPC3, jouait un rôle dans la fibrose auriculaire en favorisant l'activation des fibroblastes et ii) étudié le rôle potentiel des miARNs dans ce contexte. Nous avons démontré que les canaux TRPC3 favorisent l’influx du Ca2 +, activant la signalisation Ca2 +-dépendante ERK et en conséquence activent la prolifération des fibroblastes. Nous avons également démontré que l’expression du TRPC3 est augmentée dans la FA et que le blocage in vivo de TRPC3 empêche le développement de substrats reliés à la FA. Nous avons par ailleurs validé que miR-26 régule les canaux TRPC3 en diminuant leur expression dans les fibroblastes. Enfin, nous avons montré que l'expression réduite du miR-26 est également due à l’activité augmentée de NFATc3/c4 dans les fibroblastes, expliquant ainsi l’augmentation de TRPC3 lors de la FA, confirmant la contribution de miR-26 dans le processus de remodelage structurel lié à la FA. En conclusion, nos résultats mettent en évidence l'importance des miARNs dans la régulation des canaux ioniques cardiaques. Notamment, miR-26 joue un rôle important dans le remodelage électrique et structurel associé à la FA et ce, en régulant IK1 et l’expression du canal TRPC3. Notre étude démasque ainsi un mécanisme moléculaire de contrôle de la FA innovateur associant des miARNs. miR-26 en particulier représente apres ces travaux une nouvelle cible thérapeutique prometteuse pour traiter la FA. / Atrial fibrillation (AF) is the most frequently-encountered arrhythmia in clinical practice and constitutes a major cause of cardiac morbidity and mortality. The management of AF remains a major challenge as current therapeutic approaches are limited by potential adverse effects and high rate of AF recurrence/persistence. A better understanding of the mechanisms underlying AF is of great importance to improve AF therapy. AF is characterized by impaired electrical and structural remodeling, both of which favors the recurrence and maintenance of the arrhythmia. A key feature in electrical remodeling is the reduced atrial effective refractory period, due to ion channel alteration. Structural remodeling, on the other hand, mainly results from atrial fibrosis. However, the precise molecular mechanisms underlying these remodeling processes are still incompletely understood. The importance of microRNAs (miRNAs) in various pathophysiological conditions of the heart has been well established, but little is known with regard to cardiac arrhythmias. Emerging evidence suggests that dysregulation of miRNAs may underlie heart rhythm disturbances. The aim of the present work was to acquire a comprehensive understanding of miRNA-mediated regulation of ion channels in cardiac arrhythmias. Notably, we will focus on the mechanistic insights of miRNAs related to the control of AF. Currently available experimental approaches do not permit thorough characterization of miRNA targeting. For this purpose, we performed bioinformatic analyses in conjunction with experimental approaches to identify miRNAs from the database that potentially regulate human cardiac ion channel genes. We found that only a subset of miRNAs target cardiac ion channel genes. Based on these results, we further demonstrated that the dysregulation of ion channel gene expression observed in various cardiac disorders (e.g. cardiomyopathy, myocardial ischemia, and atrial fibrillation) can be explained by the dysregulation of miRNAs. These findings further support the potential implication of miRNAs in arrhythmogenesis under these cardiac conditions. The upregulation of the cardiac inward rectifying potassium current, IK1, is a key determinant of adverse atrial electrical remodeling associated with AF. The molecular mechanisms underlying this ionic remodeling are poorly understood. We hypothesized that altered miRNA expression is responsible for IK1 upregulation in AF. We found that miR-26 is significantly downregulated in AF and regulates IK1 by controlling the expression of its underlying subunit Kir2.1. Moreover, we demonstrated that miR-26 is under the transcriptional repression of the nuclear factor of activated T cells (NFAT) and enhanced activities of members of the NFAT family, NFATc3/c4, results in miR-26 downregulation, which accounts for IK1 enhancement in AF. Furthermore, we observed that in vivo interference of miR-26 affects AF susceptibility via the regulation of IK1, suggesting an important role of miR-26 in atrial electrical remodeling. Atrial fibrosis is a major constituent in AF-associated adverse atrial structural remodeling, involving the activation of fibroblasts and cellular Ca2+ entry. Here, we sought to determine whether the Ca2+ permeable channel, TRPC3, plays a role in AF-induced fibrosis by promoting fibroblast activation. Furthermore, we investigated the potential role of miRNAs in this context. We found that TRPC3 channels promote Ca2+-entry, which results in activation of Ca2+-dependent ERK-signaling and consequently fibroblast activation. We also demonstrated that TRPC3 is upregulated in AF and in vivo TRPC3 blockade suppresses the development of AF-promoting substrate. Furthermore, we observed that miR-26 regulates TRPC3 channels via controlling the expression of the underlying channel subunit and is downregulated in AF-fibroblasts. Finally, we showed that the reduced expression of miR-26 is also due to the enhanced NFATc3/c4 activities in AF-fibroblasts and accounts for AF-induced upregulation of TRPC3, suggesting the potential contribution of miR-26 in AF-related adverse structural remodeling process. In conclusion, our findings emphasize the importance of miRNAs in the regulation of cardiac ion channels. Notably, miR-26 plays a crucial role in AF-associated electrical and structural remodeling via the regulation of IK1 and TRPC3 channel genes. Thus, our study unravels a novel molecular control mechanism of AF at the miRNA level, suggesting miR-26 as a new and promising therapeutic target for AF.

There is a huge unmet clinical need to treat damaged articular cartilage such as that caused by osteoarthritis (OA) with an estimated 8.75 million people in the UK having sought treatment for OA (ARUK 2013). Embryonic stem cells (ESCs) offer a promising alternative therapeutic approach, potentially providing an unlimited source of chondrocytes capable of regenerating the damaged cartilage however this is limited by the efficiency of the chondrogenic differentiation protocol. An improved understanding of the posttranscriptional regulation of chondrogenesis by microRNAs (miRNAs) may enable us to improve hESC chondrogenesis. Also the recent discovery that miRNAs are selectively packaged into exosomes which can then be transferred to and be functionally active within neighbouring cells suggests they may have a role in cell-cell communication. This project investigated the regulation of miRNA expression in relation to the transcriptome during hESCs-directed chondrogenesis and the possible role for exosomes during differentiation and in stem cell maintenance of hESCs. Small RNA-seq and whole transcriptome sequencing was performed on distinct stages of hESC-directed chondrogenesis using the Directed Differentiation Protocol (DDP) developed in our lab. Also small RNA-seq was performed on exosomes isolated from hESCs and chondroprogenitors along with the donor cells that the exosomes originated from. This revealed significant changes in the expression of several miRNAs during hESC-directed chondrogenesis including: upregulation of miRNAs transcribed from the four Hox complexes, known cartilage associated miRNAs and the downregulation of pluripotency associated miRNAs. Overall miRome and transcriptome analysis revealed the two hESC lines exhibited slightly different miRome and transcriptome profiles during chondrogenesis, with Man7 displaying larger changes in miRNA and mRNA expression as it progressed through the DDP suggesting it may be more predisposed to undergo chondrogenesis. Integration of miRomes and transcriptomes generated during hESC-directed chondrogenesis identified four key functionally related clusters of co-expressed miRNAs and protein coding genes: pluripotency associated cluster, primitive streak cluster, limb development cluster and an extracellular matrix cluster. Further investigation of these gene/miRNA clusters allowed the identification of several potential novel regulators of hESC-directed chondrogenesis. In accordance with the reported literature the exosomal miRNAs from hESCs and hESC-chondroprogenitors were enriched with a guanine rich motif. Notably, several of these were enriched with targets associated with embryonic skeletal system development suggesting they may play a role in regulating differentiation. Preliminary functional experiments examining pluripotency-associated exosomes suggests they may have a role in regulating hESC stem cell maintenance. However the molecular mechanism by which this is achieved has not been investigated. This research identified main miRome and transcriptome changes during hESC-directed chondrogenesis leading to the identification of several potential novel regulators of chondrogenesis and pluripotency which can be further investigated. This project has also highlighted the potential of exosomal miRNAs to regulate hESC stem cell maintenance and differentiation.

In the first part of this dissertation, copper bimetallic corrosion and its inhibition in cleaning processes involved in interconnect fabrication is explored. In microelectronics fabrication, post chemical mechanical polishing (CMP) cleaning is required to remove organic contaminants and particles left on copper interconnects after the CMP process. Use of cleaning solutions, however, causes serious reliability issues due to corrosion and recession of the interconnects. In this study, different azole compounds are explored and pyrazole is found out to be a potentially superior Cu corrosion inhibitor, compared to the most widely used benzotriazole (BTA), for tetramethyl ammonium hydroxide (TMAH)-based post CMP cleaning solutions at pH 14. Micropattern corrosion screening results and electrochemical impedance spectroscopy (EIS) revealed that 1 mM Pyrazole in 8 wt% TMAH solution inhibits Cu corrosion more effectively than 10 mM benzotriazole (BTA) under same conditions. Moreover, water contact angle measurement results also showed that Pyrazole-treated Cu surfaces are relatively hydrophilic compared to those treated with BTA/TMAH. X-ray photoelectron spectroscopy (XPS) analysis supports Cu-Pyrazole complex formation on the Cu surface. Overall Cu corrosion rate in TMAH-based highly alkaline post CMP cleaning solution is shown to be considerably reduced to less than 1Å/min by addition of 1 mM Pyrazole. In the second part, a novel technique built in-house called multiple internal Reflection Infrared Spectroscopy (MIR-IR) was explored as a characterization tool for characterization of different low-k structures.In leading edge integrated circuit manufacturing, reduction of RC time delay by incorporation of porous ultra low-k interlayer dielectrics into Cu interconnect nanostructure continues to pose major integration challenges. The main challenge is that porous structure renders interlayer dielectrics mechanically weak, chemically unstable and more susceptible to the RIE plasma etching damages. Besides the challenge of handling weak porous ultra low-k materials, a lack of sensitive metrology to guide systematic development of plasma etching, restoration and cleaning processes is the major stumbling block. We explored Multiple Internal Reflection Infrared Spectroscopy and associated IR techniques as a sensitive (sub-5 nm) characterization tool to investigate chemical bonding modification across fluorocarbon etch residues and low-k dielectric interface after plasma etching, ashing, UV curing and post-etch cleaning. The new insights on chemical bonding transformation mapping can effectively guide the development of clean-friendly plasma etch for creating ultra low-k dielectric nanostructures with minimal dielectric damages.

This paper discusses design and implementation of classifying system for recognition of musical instruments from audio records with use of Musical Information Retrieval techniques. In the first part, paper describes parameters used for instrument classification, calculation of said parameters from records and reduction of feature vector. Next part is devoted to tuning and implementation of various classifiers with focus on neural networks. These classifiers ar further tested on records from IRMAS dataset wchich contain 11 musical instruments playing solo or with other instruments. Results of classifiers tested on different parameters and different numbers of instruments are discussed in the last part.

Background: The sensitivity to drug-induced QT prolongation is highly variable in heart failure (HF) patients. QT interval prolongation can lead to a life-threatening ventricular arrhythmia known as torsade de Pointes (TdP), which can result in sudden cardiac death. Although QT prolongation is a surrogate marker for sudden cardiac death, the extent of drug-induced QT prolongation, and thus TdP, is largely unpredictable. Therefore, developing a biomarker to predict patients’ sensitivity to drug-induced QTc prolongation could have a profound clinical impact. MicroRNA (miR) are recognized as important regulators of cardiovascular function as they shape the transcriptome by targeting mRNAs for repression of translation. Our multidisciplinary research group has demonstrated that miR-362-3p regulates a potassium channel (i.e., hERG) that is the most widely implicated in drug-induced QTc prolongation. The primary objects of this analysis focus on characterizing serum miR-362-3p expression in the circulation as a potential biomarker to predict subject’s susceptibility to ibutilide exposure induced QT-interval prolongation.<div><br></div><div>Methods: The dataset utilized to develop the PK-PD models were collected from a previous clinical study carried out by Tisdale et al. (Tisdale,et al. 2020).A total of 22 adult subjects who met the inclusion and exclusion criteria were enrolled and divided into three groups: a group of patients with heart failure with preserved ejection fraction (HFpEF, n=10), a group of patients with heart failure with reduced ejection fraction (HFrEF, n=2), and ten healthy subjects in the control group who were matched to subjects in the HFpEF group for age and sex. Following a baseline day of triplicate 12-lead ECGs, all subjects received ibutilide 0.003mg/kg intravenously infused over 10 minutes. Serial collection of blood samples to determine serum Ibutilide concentrations (HPLC/MS), serum miR-362-3 expression (qPCR), with triplicate ECG readings were obtained pre-and-post ibutilide administration. To describe ibutilide serum concentration exposure and the9relationship with Fridericia-corrected QT (QTF) intervals, a non-linear mixed effect modeling approach was used along with clinical and demographic data, and serum miR-362-3p expression was evaluated as potential covariates on the PK/PD model.<div><br></div><div>Results: A three-compartment model best described the time course of ibutilide concentrations profile with a proportional residual error. The individual ibutilide concentrations time profile was then used in an indirect response model where ibutilide concentrations are indirectly driving the QT interval prolongation through inhibition of the output (Kout) parameters linked to an indirect response model with zero‐order input parameter best described the ibutilide concentrations QT interval lengthening relationship. The Individual PK/PD parameters using the base model for the Imax and IC50 were 11.4% (9.9%RES) and 0.36(8.4% RES)ng/mL, respectively. Following stepwise forwarding inclusion steps, the final covariate analyses identified circulating miR-362-3p expression associated with a history of myocardial infarction covariate influencing both the Imax and IC50( p<0.05). <div><br></div><div>Conclusions: An indirect response model has been developed to describe the effects of ibutilide concentrations on QT-intervals. Although the semi-mechanistic model could not be developed; serummiR-362-3p expression was identified as a significant predictor for ibutilide-induced QT-interval prolongation. Moreover, the upregulation of serum miR-362-3p expression enhanced IC50 seen after ibutilide administration. The potential use of miR-362-3p as a biomarker warrants further investigation to identify patients at the greatest risk of TdP </div></div></div>

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