Cohesion decay: quantitative analysis of partial sister chromatid cohesion

Cell division is a highly dynamic process where sister chromatids remain associated with each other from the moment of DNA replication until the later stages of mitosis, giving rise to two daughter cells with equal genomes. The “molecular glue” that links sister DNA molecules is called cohesin, a tripartite ring-like protein complex composed of two Structural Maintenance of Chromosome proteins (Smc1 and Smc3) bridged by a kleisin subunit Rad21/Scc1, that together prevent precocious sister chromatid separation. Accumulating evidence has suggested that cohesion decay may be the cause of segregation errors that underlie certain human pathologies. However it remains to be determined how much cohesin loss abolishes functional sister chromatid cohesion. To answer these questions, we have developed different experimental conditions aiming to titrate the levels of cohesin on mitotic chromosomes in a precise manner. Using these tools, we will determine the minimal amount of cohesin needed to confer functional cohesion. The approaches described here take advantage of a system in Drosophila melanogaster where the Tobacco Etch Virus (TEV) protease can cleave the Rad21 subunit of cohesin leading to precocious sister chromatid separation. Firstly, we tried to express different levels of TEV protease to obtain partial loss of cohesion. However, this approach has failed to produce systematic different levels of sister chromatid separation. Most of the work was therefore focused on a second strategy, for which we established strains with different levels of cohesin sensitive/cohesin resistant to TEV protease. Strains containing different amounts of functional cohesin (TEV resistant) were tested by in vitro cleavage and by in vivo injections in embryos for their ability to promote sister chromatid cohesion. Our results reveal that removal of half of the cohesin complexes does not impair chromosome segregation, implying that chromosome cohesion is less sensitive to cohesin amounts than previously anticipated.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Dynamic stiffness of the piled foundation of a onshore wind turbine

One of today's biggest concerns is the increase of energetic needs, especially in the developed countries. Among various clean energies, wind energy is one of the technologies that assume greater importance on the sustainable development of humanity. Despite wind turbines had been developed and studied over the years, there are phenomena that haven't been yet fully understood. This work studies the soil-structure interaction that occurs on a wind turbine's foundation composed by a group of piles that is under dynamic loads caused by wind. This problem assumes special importance when the foundation is implemented on locations where safety criteria are very demanding, like the case of a foundation mounted on a dike. To the phenomenon of interaction between two piles and the soil between them it's given the name of pile-soil-pile interaction. It is known that such behavior is frequency dependent, and therefore, on this work evaluation of relevant frequencies for the intended analysis is held. During the development of this thesis, two methods were selected in order to assess pile-soil-pile interaction, being one of analytical nature and the other of numerical origin. The analytical solution was recently developed and its called Generalized pile-soil-pile theory, while for the numerical method the commercial nite element software PLAXIS 3D was used. A study of applicability of the numerical method is also done comparing the given solution by the nite element methods with a rigorous solution widely accepted by the majority of the authors.

Study of the electromyographic signal dynamic behavior in Amyotrophic Lateral Sclerosis (ALS)

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by motor neurons degeneration, which reduces muscular force, being very difficult to diagnose. Mathematical methods are used in order to analyze the surface electromiographic signal’s dynamic behavior (Fractal Dimension (FD) and Multiscale Entropy (MSE)), evaluate different muscle group’s synchronization (Coherence and Phase Locking Factor (PLF)) and to evaluate the signal’s complexity (Lempel-Ziv (LZ) techniques and Detrended Fluctuation Analysis (DFA)). Surface electromiographic signal acquisitions were performed in upper limb muscles, being the analysis executed for instants of contraction for ipsilateral acquisitions for patients and control groups. Results from LZ, DFA and MSE analysis present capability to distinguish between the patient group and the control group, whereas coherence, PLF and FD algorithms present results very similar for both groups. LZ, DFA and MSE algorithms appear then to be a good measure of corticospinal pathways integrity. A classification algorithm was applied to the results in combination with extracted features from the surface electromiographic signal, with an accuracy percentage higher than 70% for 118 combinations for at least one classifier. The classification results demonstrate capability to distinguish members between patients and control groups. These results can demonstrate a major importance in the disease diagnose, once surface electromyography (sEMG) may be used as an auxiliary diagnose method.

Analysis and visualization of energy use for university campus

The reduction of greenhouse gas emissions is one of the big global challenges for the next decades due to its severe impact on the atmosphere that leads to a change in the climate and other environmental factors. One of the main sources of greenhouse gas is energy consumption, therefore a number of initiatives and calls for awareness and sustainability in energy use are issued among different types of institutional and organizations. The European Council adopted in 2007 energy and climate change objectives for 20% improvement until 2020. All European countries are required to use energy with more efficiency. Several steps could be conducted for energy reduction: understanding the buildings behavior through time, revealing the factors that influence the consumption, applying the right measurement for reduction and sustainability, visualizing the hidden connection between our daily habits impacts on the natural world and promoting to more sustainable life. Researchers have suggested that feedback visualization can effectively encourage conservation with energy reduction rate of 18%. Furthermore, researchers have contributed to the identification process of a set of factors which are very likely to influence consumption. Such as occupancy level, occupants behavior, environmental conditions, building thermal envelope, climate zones, etc. Nowadays, the amount of energy consumption at the university campuses are huge and it needs great effort to meet the reduction requested by European Council as well as the cost reduction. Thus, the present study was performed on the university buildings as a use case to: a. Investigate the most dynamic influence factors on energy consumption in campus; b. Implement prediction model for electricity consumption using different techniques, such as the traditional regression way and the alternative machine learning techniques; and c. Assist energy management by providing a real time energy feedback and visualization in campus for more awareness and better decision making. This methodology is implemented to the use case of University Jaume I (UJI), located in Castellon, Spain.

Maritime Security in the Gulf of Guinea: Issues and Solutions for the 21st Century

A producer of 5.4 M bbl/d, totalling almost half of the consumption of the entire European Union, the Gulf of Guinea is a fundamental lifeline and maritime link between Europe, the Americas and Africa. Geographically positioned as a staging post for transit originating in Latin America and coupled with its relatively porous borders, the region is also the perfect stepping stone for contraband heading to European shores. While blessed with an enviable wealth of marine and mineral resources, the region is also plagued by an ever-increasing spectre of maritime piracy; accounting for around 30% of incidents in African waters from 2003 to 2011. It is for these reasons that this research centres around the issues of maritime security in the Gulf of Guinea, with a particular focus on the first two decades of the 21st century. This research looks to examine the overall picture of the present state of play in the area, before going on to provide an analysis of potential regional developments in maritime security. This research begins with the analysis of concepts/phenomena that have played a notable role in the shaping of the field of maritime security, namely Globalisation and security issues in the post-Cold War era. The ensuing chapter then focuses in on the Gulf of Guinea and the issues dominating the field of maritime security in the region. The penultimate chapter presents a SWOT analysis, undertaken as part of this research with the aim of correlating opinions from a variety of sectors/professions regarding maritime security in the Gulf of Guinea. The final chapter builds upon the results obtained from the abovementioned SWOT analysis, presenting a series of potential proposals/strategies that can contribute to the field of maritime security in the region over the coming years. This research draws to a close with the presentation of conclusions taken from this particular investigation, as well as a final overview of the earlier presented proposals applicable to the field of maritime security during the second decade of the 21st century.

Relatório de estágio na Caixa Geral de Depósitos

This report will describe the activities undertaken during my internship at the Personnel Department (DPE-UPE4.1) in Caixa Geral de Depósitos (CGD), Lisbon, between September 22, 2014, and February 28, 2015. I consider that it is important to note from the outset i) that the subject of my training was suggested by my supervisor in the DPE and accepted by me; and ii) that the internship consisted essentially of carrying out research and information gathering into the different social systems that coexist within the bank and the application of each legal system in solving concrete situations of the CGD employees. The research and analysis of information was important not only for my study but for the CGD itself, as it enables the department to have such an important matter, full of specific characteristics, condensed into a single document, i.e. this report. This is a complex reality. The various welfare systems differ according to the contractual agreement linking the employee to the employer at the date when the labour contract is signed, and also the unique/singular characteristics of the CGD. In the early stage I started by trying to understand the financial institution and its organization and role and the department where I worked. So I analyzed the CGD Statutes and the legal measures that crystallized the scheme for its employees and I also researched its domestic and international operations. The first month was devoted to the research and analysis of such legislation to understand the creation of the CGD and its path to date. In the second and third months I studied the legal social systems that are applied to different groups of CGD workers. This period was quite important to identify and understand the differences between those regimes of CGD employees as well as the procedure inherent in each case. I highlighted the non-implementation of “the social protection regime of convergence” to the workers of this institution; the differences regarding the allocation of sickness subsidies paid to workers who belong to Social Security and CGA contributors, as well as the enforcement of internal rules to all the workers when a work-related accident happens. Then I focused on to assessing and examining external legislation and several internal regulations in order to obtain solutions to questions raised and situations involving by the workers, in order to understand how the DPE solves these situations. Over the last three months of internship, after this more theoretical work, I began the analysis of concrete situations involving employees carrying out their duties in Portugal and abroad. Some of these situations had been received by the department before the beginning of my internship and others over this period. When I was “working” in the DPE I analyzed “cases” that had been solved and some others without a final solution because they were still in courts. As for the last ones (new cases) I was able to follow their assessment and sometimes their outcome. Some of them became study cases for me. Over these five months of my internship, several cases were analyzed and discussed by legal experts of DPE in which I could participate. I always worked hard. I know that this action contributed to elucidate me about the treatment of the issues, and allowed me to have a direct contact with some workers and be part of a dynamic work team. For these reasons, my internship report is not merely descriptive of activities. It consists of an analysis of rules (legislation) and a regulatory framework of activities and it is also a description of several specific situations solved or in a solution process. Through this work I intend to make known the particular reality of a modern Portuguese financial institution not only because of its importance in our country but also such a large number of employees work here (in Portugal and abroad). I should add that throughout my internship I was allowed to attend conferences, within the scope of the bank in order to get a broader view of some issues related to the daily life of the DPE and the CGD. So, I participated in I Jornadas Bancárias and the Conferência Internacional do Contrato a Termo, given that the CGD is a bank and the DPE deals with legal and labour relations.

Managing marginal capital requirements in solvency II: Analysis of a real insurance portfolio

This thesis provides a complete analysis of the Standard Capital Requirements given by Solvency II for a real insurance portfolio. We analyze the investment portfolio of BPI Vida e Pensões, an insurance company affiliated with a Portuguese bank BPI, both at security, sub-portfolio and asset class levels. By using the Standard Formula from EIOPA, Total SCR amounts to 239M€. This value is mostly explained by Market and Default Risk whereas the former is driven by Spread and Concentration Risks. Following the methodology of Leblanc (2011), we examine the Marginal Contribution of an asset to the SCR which allows for the evaluation of the risks of each security given its characteristics and interactions in the portfolio. The top contributors to the SCR are Corporate Bonds and Term Deposits. By exploring further the composition of the portfolio, our results show that slight changes in allocation of Term and Cash Deposits have severe impacts on the total Concentration and Default Risks, respectively. Also, diversification effects are very relevant by representing savings of 122M€. Finally, Solvency II represents an opportunity for the portfolio optimization. By constructing efficient frontiers, we find that as the target expected return increases, a shift from Term Deposits/ Commercial Papers to Eurozone/Peripheral and finally Equities occurs.

Future lending income and security value

I test the Duffie, Gârleanu, and Pedersen hypothesis that security prices incorporate expected future securities lending income. To determine whether institutional investors anticipate gains from future lending of securities, I examine their trading behavior around loan-fee increases. The evidence suggests that institutions buy shares in response to an increase in lending fees, and that this could explain the premium associated with high- lending-fee stocks. Expected future lending income affects stock prices, although the effect seems to be attenuated by the negative information that arises from short selling.

Analysis of a controversial decision process: the case of the pumped hydro storage power plant Atdorf in Germany

Based on the report for the unit “Métodos Interactivos de Participação e Decisão A” (Interactive methods of participation and decision A), coordinated by Prof. Lia Maldonado Teles de Vasconcelos and Prof. Nuno Miguel Ribeiro Videira Costa. This unit was provided for the PhD Program in Technology Assessment in 2015/2016.

Relatório de estágio na Caixa Geral de Depósitos

This report will describe the activities undertaken during my internship at the Personnel Department (DPE-UPE4.1) in Caixa Geral de Depósitos (CGD), Lisbon, between September 22, 2014, and February 28, 2015. I consider that it is important to note from the outset i) that the subject of my training was suggested by my supervisor in the DPE and accepted by me; and ii) that the internship consisted essentially of carrying out research and information gathering into the different social systems that coexist within the bank and the application of each legal system in solving concrete situations of the CGD employees. The research and analysis of information was important not only for my study but for the CGD itself, as it enables the department to have such an important matter, full of specific characteristics, condensed into a single document, i.e. this report. This is a complex reality. The various welfare systems differ according to the contractual agreement linking the employee to the employer at the date when the labour contract is signed, and also the unique/singular characteristics of the CGD. In the early stage I started by trying to understand the financial institution and its organization and role and the department where I worked. So I analyzed the CGD Statutes and the legal measures that crystallized the scheme for its employees and I also researched its domestic and international operations. The first month was devoted to the research and analysis of such legislation to understand the creation of the CGD and its path to date. In the second and third months I studied the legal social systems that are applied to different groups of CGD workers. This period was quite important to identify and understand the differences between those regimes of CGD employees as well as the procedure inherent in each case. I highlighted the non-implementation of “the social protection regime of convergence” to the workers of this institution; the differences regarding the allocation of sickness subsidies paid to workers who belong to Social Security and CGA contributors, as well as the enforcement of internal rules to all the workers when a work-related accident happens.Then I focused on to assessing and examining external legislation and several internal regulations in order to obtain solutions to questions raised and situations involving by the workers, in order to understand how the DPE solves these situations. Over the last three months of internship, after this more theoretical work, I began the analysis of concrete situations involving employees carrying out their duties in Portugal and abroad. Some of these situations had been received by the department before the beginning of my internship and others over this period. When I was “working” in the DPE I analyzed “cases” that had been solved and some others without a final solution because they were still in courts. As for the last ones (new cases) I was able to follow their assessment and sometimes their outcome. Some of them became study cases for me. Over these five months of my internship, several cases were analyzed and discussed by legal experts of DPE in which I could participate. I always worked hard. I know that this action contributed to elucidate me about the treatment of the issues, and allowed me to have a direct contact with some workers and be part of a dynamic work team. For these reasons, my internship report is not merely descriptive of activities. It consists of an analysis of rules (legislation) and a regulatory framework of activities and it is also a description of several specific situations solved or in a solution process. Through this work I intend to make known the particular reality of a modern Portuguese financial institution not only because of its importance in our country but also such a large number of employees work here (in Portugal and abroad). I should add that throughout my internship I was allowed to attend conferences, within the scope of the bank in order to get a broader view of some issues related to the daily life of the DPE and the CGD. So, I participated in I Jornadas Bancárias and the Conferência Internacional do Contrato a Termo, given that the CGD is a bank and the DPE deals with legal and labour relations.