Kinetic Intersections as a Source of Information on Rate Coefficients

C

Improvements to the nitrogen dioxide observations by means of the MKIV Brewer spectrophotometer

Nitrogen dioxide (NO2) is a key component of the Earth's atmosphere, being involved in the ozone destruction and production and influencing the radiative balance of our planet. Furthermore, it impacts on human health and contributes to the tropospheric pollution. Techniques to measure atmospheric nitrogen dioxide from both the space and the ground have noticeably advanced in the last decades and provide valuable information, while also presenting some serious limitations. In 1985, an automated Brewer ozone spectrophotometer was modified to add capability to measure solar visible radiation and retrieve atmospheric nitrogen dioxide besides total ozone and sulfur dioxide. Since then, more than 60 MKIV Brewer spectrophotometers have been put in operation in a worldwide network and long-term nitrogen dioxide records have been collected at several sites. However, the original algorithm, developed in the 1980's, has never been officially updated and, although notable efforts have been done in the last years to improve the retrieval by the Brewer, high-quality estimates of nitrogen dioxide by this instrument are still difficult to acquire. This work introduces substantial innovation in measuring nitrogen dioxide with MKIV Brewers. For the first time, an instrument of this type was thoroughly characterised in its operating spectral range. A novel mathematical framework supporting observations was then developed to update the Brewer processing algorithm, to better understand its potentials and limitations and to optimise the measurement technique. The spectroscopic data sets used within the algorithm were completely updated using the most recently published absorption cross sections. Model calculations were performed with top-level radiative transfer codes to test the new algorithm, which not only allows more accurate estimates of nitrogen dioxide, but also introduces new capabilities in Brewer measurements, such as the retrieval of the oxygen dimer (O4) and the degree of the linear polarisation of skylight. To test the new method, four field campaigns were organised. The limitations in the traditional calibration techniques due to the daily evolution of nitrogen dioxide were overcome by employing an innovative method and one Brewer (#066) was successfully calibrated and compared to an instrument belonging to the Network for the Detection of Atmospheric Composition Change. The two different observation techniques in which the Brewer operates, namely by looking directly to the sun or vertically to the zenith, were proven to be equivalent within the stated uncertainty. The latter was thoroughly evaluated by means of a Monte Carlo based method. The new algorithm was effectively applied to reprocess the long-term series recorded in the European Brewer stations of Saint-Christophe and Rome (Italy), Athens (Greece), Hradec Kralove (Czech Republic). To this purpose, two empirical methods to calibrate the Brewer instruments through statistical analyses were validated. The results were compared with satellite total column data retrieved from the SCIAMACHY, GOME-2 and OMI instruments and with in-situ measurements of tropospheric concentrations to assess the impact of anthropogenic emissions

Proteomics of Poly(ADP-ribose) Polymerases during DNA Replication and Repair

En 2017, Statistique Canada a rapporté qu'un Canadien sur quatre mourra d’un cancer. Chaque jour, nous sommes confrontés à des facteurs environnementaux qui imposent à notre ADN un stress génotoxique. Ce stress peut avoir de graves conséquences au point de menacer notre intégrité génomique, comme les cassures d'ADN double-brin (DSBs). Heureusement, nos cellules ont deux voies principales pour combattre ce type de lésions : la recombinaison homologue (HR) et la Classical Non-Homologous End-Joining (CNHEJ). La voie HR, un type de réparation sans erreur utilisé dans la phase-S du cycle cellulaire, assure une réparation fidèle de la zone endommagée et conserve l'intégrité de l'information génétique. Les individus porteurs de mutations dans les protéines de cette voie, telles que BRCA1 et BCRA2, sont plus susceptibles de développer des cancers du sein et de l'ovaire. Récemment, la clinique a connu une percée majeure dans le traitement du cancer de l'ovaire. Une nouvelle classe de médicaments a été autorisée par la US Food and Drug Administration (FDA) pour traiter les cancers de l'ovaire récurrents qui présentent une HR défective. Ces médicaments inhibent un des acteurs les plus précoces dans la réponse aux dommages à l'ADN (DDR): la PARP-1 (Poly(ADP-ribose) polymerase-1). Lors de l'induction de dommages à l'ADN, la PARP-1 devient fortement activée, conduisant à la production massive de polymères de poly(ADP-ribose) (PAR) générés à partir de l'hydrolyse du nicotinamide adénine dinucléotide. Ce polymère agira comme une plateforme pour recruter des facteurs de réparation de l'ADN au site de réparation. L'application clinique réussie des inhibiteurs de la PARP (PARPi) vient des observations où les mutations ou l'extinction de BRCA1/2 entraînent une diminution de l'activité HR. L'inhibition de la PARP-1 combinée à cette déficience en HR favorise la mort cellulaire, un phénomène appelé létalité synthétique. Trois PARPi sont actuellement autorisés par la FDA et sont utilisés pour le traitement du cancer gynécologique. Malgré l'efficacité thérapeutique de ces inhibiteurs, les mécanismes induisant une régression tumorale ne sont pas complètement compris. Ainsi, il devient extrêmement important de déchiffrer davantage ces mécanismes pour atteindre le plein potentiel des PARPi. Pour ce faire, une recherche fondamentale sur les fonctions des PARPs, et de leurs partenaires dans la DDR, est essentielle et constitue l'objectif général de cette thèse. Durant mon doctorat, nous avons étudié l'influence de la PARP-1 dans la voie HR au moment de l'étape initiale de la résection, qui est essentielle pour l'élimination de l'ADN endommagé. Certaines études ont montré l'implication de la PARP-1 dans le recrutement de la protéine de résection MRE11. Ici, nous démontrons que la PARP-1 a une nouvelle fonction dans la résection des DSBs et nous proposons un nouveau modèle pour expliquer la létalité synthétique observée dans les tumeurs avec une HR défective. Pour compléter l'objectif de ce doctorat, nous avons étudié les rôles régulateurs de la PARP-1 au cours du processus HR, mais plus tard dans la résolution des lésions, c'est-à-dire au maximum de la formation des foyers RAD51, une étape cruciale pour la réparation efficace des DSBs via la HR. Nous avons observé que le PAR-interactome (PARylome) est, à ce moment, fortement enrichi en protéines impliquées dans le métabolisme de l'ARN. Plusieurs des protéines les plus abondantes étaient constituées d’hélicases d’ADN et d’ARN, et de facteurs de transcription. Puisque certains de ces gènes sont mutés dans les tumeurs, ils pourraient théoriquement être des cibles prioritaires pour une utilisation conjointe avec des PARPi. Nous avons également étendu notre étude de la PARylation à la chromatine, au niveau des histones. Nous avons constaté que les queues d'histones ne sont pas les seules cibles de la PARP-1 et que les domaines globulaires centraux sont également PARylés. Finalement, le grand intérêt clinique de la PARP-1 méritait une analyse approfondie de son expression systémique. Ainsi, j'ai terminé mes études en décrivant la distribution et l'abondance tissulaire de la PARP-1 dans les organes simiens, avec l'objectif principal de fournir des informations précieuses quant à l'efficacité potentielle des PARPi ou sa résistance, dans un tissu donné et maladies apparentées. En résumé, cette thèse fournit de nouvelles informations importantes sur les mécanismes orchestrés par la PARP-1 lors de la réponse aux DSBs, y compris les réseaux protéiques complexes engagés dans le remodelage des fonctions cellulaires nécessaire au maintien de l'intégrité génomique.In 2017, Statistics Canada reported that one out of four Canadians will die of cancer. Every day, we face environmental factors that burden our DNA with genotoxic stress. This stress can lead to severe types of DNA damage that can threaten our genomic integrity, namely double-strand breaks (DSBs). Fortunately, our cells have evolved with different repair mechanisms to deal with such lesions. There are two primary types of repair against DSBs: Homologous Recombination (HR) and Classical Non-Homologous End-Joining (CNHEJ). The HR pathway is an error-free repair mechanism used in the S-phase of the cell cycle to ensure faithful repair of the damaged area and thus preserve our genetic information. Individuals that bear mutations in proteins involved in this pathway, such as BRCA1 and BCRA2, have been associated with the development of breast and ovarian cancers. Almost 4 years ago, the field went through a major breakthrough in ovarian cancer care. A new class of drugs was accepted by the US Food and Drug Administration (FDA) to manage recurrent ovarian cancers that display HR-deficiencies. These drugs consist of inhibitor molecules against one of the earliest sensors of DNA damage in the cell: PARP-1 (poly(ADP-ribose) polymerase-1). Upon DNA damage induction, PARP-1 becomes highly activated, leading to the massive production of poly(ADP-ribose) (PAR) polymers, from the hydrolysis of nicotinamide adenine dinucleotide, which in turn modify several proteins posttranslationally and act as a scaffold to recruit DNA repair factors to the repair site. The successful application of PARP inhibitors (PARPi) arose from the observations that mutations or silencing of BRCA1/2, resulted in diminished HR activity. In the context of HR deficiency, the concomitant inhibition of PARP resulted in cell-death, an effect called synthetic lethality. Three PARPi are currently accepted by the FDA and are being clinically used for the treatment of gynaecological cancers. Notwithstanding the great promise of these inhibitors for other types of cancers, the mechanism by which these are inducing cancer lethality is not fully understood. Thus, it becomes of extreme importance to further decipher its mechanistic ways, to achieve full potential of PARPi in the clinic. To achieve this, fundamental research on the functions of PARPs and their protein partners in the DNA damage response is indispensable and constitutes the general aim of this thesis. During my doctoral work, we investigated the influence of PARP-1 during the HR pathway, primarily during the initial step of resection, which is essential for the removal of damaged DNA. Early reports of PARP-1 involvement in resection described the recruitment of the resection protein MRE11 to sites of damage in a PARP-1 dependent manner. Here, we demonstrate that PARP-1 has a novel function in DSB resection and we propose a new model for the synthetic lethality observed in HR-deficient tumors. To further complement the general aim of this doctorate, we investigated the regulatory roles of PARP-1 during the HR pathway, however in a later stage of HR resolution, at the peak formation of RAD51 foci, which is a crucial step for the efficient repair of DSBs through HR. We observed that the PAR-interactome (PARylome) at this stage was abundantly enriched with RNA-processing factors. Several of the most abundant proteins consisted of DNA and RNA helicases, as well as transcription factors, some of which were found to be mutated in tumors, and thus can be seen as potentially druggable targets to be used in combination with PARPi. We also extended our PARylome study to the chromatin proteome and investigated the histone PARylome upon DNA damage. Interestingly, we found that histone tails are not the only targets of PARP-1 and that globular domains are also targets of PARylation. Lastly, the high clinical interest of PARP-1 warrants studies addressing PARP-1 organ distribution. Thus, I finalized my studies by extensively describing and reporting PARP-1 tissular and cellular distribution and abundance in monkey organs, with the main objective of providing valuable information to any study assessing PARP inhibition efficacy and resistance in any given tissue and related diseases. In summary, this thesis provides important new information on the mechanisms PARP-1 is regulating during the response to DSBs, including the networks PARP-1 is orchestrating to potentially help reshape the cell environment, to efficiently repair the most lethal lesion our genome faces

Expanding the Horizons of Manufacturing: Towards Wide Integration, Smart Systems and Tools

This research topic aims at enterprise-wide modeling and optimization (EWMO) through the development and application of integrated modeling, simulation and optimization methodologies, and computer-aided tools for reliable and sustainable improvement opportunities within the entire manufacturing network (raw materials, production plants, distribution, retailers, and customers) and its components. This integrated approach incorporates information from the local primary control and supervisory modules into the scheduling/planning formulation. That makes it possible to dynamically react to incidents that occur in the network components at the appropriate decision-making level, requiring fewer resources, emitting less waste, and allowing for better responsiveness in changing market requirements and operational variations, reducing cost, waste, energy consumption and environmental impact, and increasing the benefits. More recently, the exploitation of new technology integration, such as through semantic models in formal knowledge models, allows for the capture and utilization of domain knowledge, human knowledge, and expert knowledge toward comprehensive intelligent management. Otherwise, the development of advanced technologies and tools, such as cyber-physical systems, the Internet of Things, the Industrial Internet of Things, Artificial Intelligence, Big Data, Cloud Computing, Blockchain, etc., have captured the attention of manufacturing enterprises toward intelligent manufacturing systems

Ensuring the in vitro degradation reproducibility of powder metallurgy processed Mg 0.6Ca system

Magnesium degradation is a complex phenomenon that is too difficult to be described by a single influential parameter. Magnesium degradation is often influenced by either overtaking or overlapping factors like the cell culture medium composition, physiological conditions, impurities, and material’s internal microstructure, etc. This poses a challenge in obtaining the reproducible degradation results. Hence, in the present work, microstructural features like porosity and grain size distributions in powder metallurgy (PM) Mg-0.6Ca system were discretely evaluated for their roles in altering the specimen in vitro degradation rates. Importance was also given to the specimen impurity and mechanical properties. Based on the results, the limitations in PM processing conditions towards obtaining robust degradation results or, in other words, the material parameter thresholds to be realized for obtaining reproducible degradation profiles in PM Mg-0.6Ca specimens were put forth. Additionally, using literature evidence, the mechanisms governing pore closure and grain growth during liquid phase sintering of Mg-0.6Ca specimens from the PM processing perspective were determined. PM Mg-0.6Ca specimens were fabricated via powder blending of pure magnesium and master alloy Mg-10Ca powders. Specimens of seven different porosities, from 3% to 21%, were produced by varying sintering temperatures. Specimens with heterogeneous grain size distributions were obtained by surface modification of pure magnesium powders by means of a mechanical sieving treatment. Degradation profiles were analyzed in vitro using a semi static immersion test for 16 days under physiological conditions of 37 °C, 20% O2, 5% CO2, 95% relative humidity. Dulbecco’s modified Eagle’s medium was used as cell culture medium with Glutamax and 10% fetal bovine serum as supplements. Mechanical properties were determined using micro tensile specimens. The results indicate that low mean degradation rates (MDR 95% to ≤ 45% when falling below this value. Similarly, the pore interconnectivity sharply drops from > 95% to < 10% at this porosity, thereby enhancing the degradation reproducibility. From PM processing perspective, the sintering temperature of 570 °C is proven as beneficial to promote liquid fractions high enough to enhance specimen sinter density. The present work also showed that heterogeneous grain growth is prompted by the reduced oxide pinning effect at the grain boundaries during sintering of PM Mg-0.6Ca specimens. The heterogeneous grain growth additionally induced the formation of eutectic lamellar structure α-Mg + Mg2Ca at certain grain boundaries throughout the microstructure, which is otherwise not evident in specimens with a homogeneous grain size. Based on the literature and results of the present work, it is postulated that this eutectic structure is the major reason for a non-reproducible degradation in PM Mg-0.6Ca specimens possessing a heterogeneous grain structure. Though mechanical properties are not majorly affected, it is recommended that heterogeneous grain growth is to be avoided in PM Mg-0.6Ca specimens. The presented results also implicitly conveyed the flexibility of PM as a viable technique to design Mg-Ca materials with tailor made degradation and mechanical strengths

On the origins of pediatric brain cancer:Exploring the role of genome instability in development and disease

Childhood brain cancerEvery year, more than 100 children are diagnosed with brain cancer in the Netherlands. Although most are cured, survivors face severe neurological problems later in life. This calls for better strategies to tackle the disease, from a better understanding of its origin to the development of treatments that target the tumor cell more specifically.Brain developmentEarly in human development, the basic brain structure of the future fetus starts to develop – lasting up to 2 years after birth. During this long period of time, brain cells divide intensively to form the entire brain structure. The division of brain cells is dependent on signaling pathways. Any deviation in those signaling pathways will hinder normal brain development. Very often, errors in these growth pathways are found in childhood brain cancer. Therefore, brain cancers in children can be defined as a developmental disease, in which normal development takes a wrong turn.Genome instabilityIn order to build a functional (brain) tissue, cells undergo an amplification process called cell division. Cell division means that the entire repertoire of genes -the genome- is passed on to two daughter cells. During each division, cells face threats that if not countered, damage the genome and lead to genome instability. Genome instability is believed to be present during normal brain development due to the high division rate of the brain cells.The work described in this thesis investigates the role of genome instability in the development of brain cancer in children. Our research paves the way for the discovery of new therapeutic targets that could be used in the future to better treat this deadly disease

Non-Linear Lattice

The development of mathematical techniques, combined with new possibilities of computational simulation, have greatly broadened the study of non-linear lattices, a theme among the most refined and interdisciplinary-oriented in the field of mathematical physics. This Special Issue mainly focuses on state-of-the-art advancements concerning the many facets of non-linear lattices, from the theoretical ones to more applied ones. The non-linear and discrete systems play a key role in all ranges of physical experience, from macrophenomena to condensed matter, up to some models of space discrete space-time

Modeling and Simulation of Lipid Membranes

Cell membranes are complex structures able to contain the main elements of the cell and to protect them from the external surroundings, becoming the most fundamental interface in Biology. The main subject of this book is the study of the structure and characteristics of lipid membranes in a wide variety of environments, ranging from simple phospholipid membranes to complex systems including proteins, peptides, or oncogenes as well as the analysis of the interactions of the membrane components with small molecules and drugs. The scope of this book is to provide recent developments on membrane structure, composition and function by means of theoretical and experimental techniques, some of them combining computer simulations with available data obtained at the laboratory.This Special Issue aims to report brand new key contributions to the field and also to give an overview about the connection between experiments and computer simulations, addressing fundamental aspects and applied research in biological membranes, with particular attention paid to the applications of computer modeling and simulation to medicine

Polymer Materials in Biomedical Application

Recently, the development of polymeric materials for biomedical applications has advanced significantly. Polymeric materials are favored in the development of therapeutic devices, including temporary implants and three-dimensional scaffolds for tissue engineering and in vitro disease modelling.Further advancements have also occurred in the utilization of polymeric materials for pharmacological applications, such as delivery vehicles for drug release.We would like to invite you to contribute to this Special Issue. Research topics of interest include, but are not limited to, recent advances related to 3D cell culture, biomaterials, tissue engineering, disease modelling, hydrogel, organoids, drug discovery, bioimaging, cardio-renal, metabolic disease, and stem cell biology