Light controlled synthesis of nucleic acids

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica - especialidade Biotecnologia, pela Universidade Nova de Lisboa,Faculdade de Ciências e Tecnologia

Insights into the role of almond CBF transcription factors in the environmental control of cold acclimation and dormancy break

Dissertation presented to obtain the Ph.D degree in Biology

Photochemical degradation of triclosan: a comparison between different light sources

New emerging contaminants could represent a danger to the environment and Humanity with repercussions not yet known. One of the major worldwide pharmaceutical and personal care productions are antimicrobials products, triclosan, is an antimicrobial agent present in most products. Despite the high removal rate of triclosan present in wastewater treatments, triclosan levels are on the rise in the environment through disposal of wastewater effluent and use of sewage sludge in land application. Regulated in the EC/1272/2008 (annex VI, table 3.1), this compound is considered very toxic to aquatic life and it has been reported that photochemical transformation of triclosan produces dioxins. In the current work it was defined three objectives; determination of the most efficient process in triclosan degradation, recurring to photochemical degradation methods comparing different sources of light; identification of the main by-products formed during the degradation and the study of the influence of the Fenton and photo-Fenton reaction. Photochemical degradation methods such as: photocatalysis under florescent light (UV), photocatalysis under visible light (sunlight), photocatalysis under LEDs, photo-Fenton and Fenton reaction have been compared in this work. The degradation of triclosan was visualized through gas chromatography/mass spectrometry (GC/MS). In this study photo-Fenton reaction has successfully oxidized triclosan to H2O and CO2 without any by-products within 2 hours. Photocatalysis by titanium dioxide (TiO2) under LEDs was possible, having a degradation rate of 53% in an 8 hours essay. The degradation rate of the Fenton reaction, UV light and sunlight showed degradation between 90% and 95%. The results are reported to the data observed without statistic support, since this was not possible during the work period. Hydroquinone specie and 2,4-dichlorophenol by-products were identified in the first hour of photocatalysis by UV. A common compound, possibly identified has C7O4H , was present at the degradation by UV, sunlight and LEDs and was concluded to be a contaminant. In the future more studies in the use of LEDs should be undertaken given the advantages of long durability and low consumption of energy of these lamps and that due to their negative impact on the environment fluorescent lamps are being progressively made unavailable by governments, requiring new solutions to be found. Fenton and photo-Fenton reactions can also be costly processes given the expensive reagents used.

Electron driven reactions in complexes embedded in superfluid helium droplets

A thesis submitted to the University of Innsbruck for the doctor degree in Natural Sciences, Physics and New University of Lisbon for the doctor degree in Physics, Atomic and Molecular Physics

Dynamic and interaction of cytochrome c with Pf1 virus

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

Development of new biomaterials based on liquid crystalline phases of cellulose derivatives

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do Grau de Mestre em Engenharia Biomédica

The role of ribonuclease R in bacterial adaptation to cold shock

RESUMO:Os microrganismos reagem à súbita descida de temperatura através de uma resposta adaptativa específica que assegura a sua sobrevivência em condições desfavoráveis. Esta adaptação inclui alterações na composição da membrana, na maquinaria de tradução e transcrição. A resposta ao choque térmico pelo frio induz uma repressão da transcrição. No entanto, a descida de temperatura induz a produção de um grupo de proteínas específicas que ajudam a ajustar/re-ajustar o metabolismo celular às novas condições ambientais. Em E. coli o processo de adaptação demora apenas quatro horas, no qual um grupo de proteínas específicas são induzidas. Depois desde período recomeça lentamente a produção de proteínas.A ribonuclease R, uma das proteínas induzidas durante o choque térmico pelo frio, é uma das principais ribonucleases em E. coli envolvidas na degradação do RNA. É uma exoribonuclease que degrada RNA de cadeia dupla, possui funções importantes na maturação e “turnover” do RNA, libertação de ribossomas e controlo de qualidade de proteínas e RNAs. O nível celular desta enzima aumenta até dez vezes após exposição ao frio e estabiliza em células na fase estacionária. A capacidade de degradar RNA de dupla cadeia é importante a baixas temperaturas quando as estruturas de RNA estão mais estáveis. No entanto, este mecanismo é desconhecido. Embora a resposta específica ao “cold shock” tenha sido descoberta há mais de duas décadas e o número de proteínas envolvidas sugerirem que esta adaptação é rápida e simples, continuamos longe de compreender este processo. No nosso trabalho pretendemos descobrir proteínas que interactuem com a RNase R em condições ambientais diferentes através do método “TAP-tag” e espectrometria de massa. A informação obtida pode ser utilizada para deduzir algumas das novas funções da RNase R durante a adaptação bacteriana ao frio e durante a fase estacionária. Mais importante ainda, RNase R poderá ser recrutada para um complexo de proteínas de elevado peso molecular durante o “cold-shock”.------------ABSTRACT:Microorganisms react to the rapid temperature downshift with a specific adaptative response that ensures their survival in unfavorable conditions. Adaptation includes changes in membrane composition, in translation and transcription machinery. Cold shock response leads to overall repression of translation. However, temperature downshift induces production of a set of specific proteins that help to tune cell metabolism and readjust it to the new environmental conditions. For Escherichia coli the adaptation process takes only about four hours with a relatively small set of specifically induced proteins involved. After this time, protein production resumes, although at a slower rate. One of the cold inducible proteins is RNase R, one of the main E. coli ribonucleases involved in RNA degradation. RNase R is an exoribonuclease that digest double stranded RNA, serves important functions in RNA maturation and turnover, release of stalled ribosomes by trans-translation, and RNA and protein quality control. The level of this enzyme increases about ten-fold after cold induction, and it is also stabilised in cells growing in stationary phase. The RNase R ability to digest structured RNA is important at low temperatures where RNA structures are stabilized but the exact role of this mechanism remains unclear. Although specific bacterial cold shock response was discovered over two decades ago and the number of proteins involved suggests that this adaptation is fast and simple, we are still far from understanding this process. In our work we aimed to discover the proteins interacting with RNase R in different environmental conditions using TAP tag method and mass spectrometry analysis. The information obtained can be used to deduce some of the new functions of RNase R during adaptation of bacteria to cold and in stationary growth phase. Most importantly RNase R can be recruited into a high molecular mass complex of protein in cold shock.

Decision making processes based on innovation indicators: which implications for technology assessment?

Based on the report for “Project IV” unit of the PhD programme on Technology Assessment. This thesis research has the supervision of António Moniz (FCT-UNL and ITAS-KIT) and Manuel Laranja (ISEG-UTL). Other members of the thesis committee are Stefan Kuhlmann (Twente University), Leonhard Hennen (Karlsruhe Institute of Technology-ITAS), Tiago Santos Pereira (Universidade de Coimbra/CES) and Cristina Sousa (FCT-UNL).

Effects of UV radiation exposure on DNA and DNA repair enzymes

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases

J Biol Inorg Chem (2011) 16:443–460 DOI 10.1007/s00775-010-0741-z

Three essays in risky behaviors

A PhD Dissertation, presented as part of the requirements for the Degree of Doctor of Philosophy from the NOVA - School of Business and Economics

Green light for green energy: Growth in spite of crisis

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

An application of reliability-based robustness assessment of steel moment resisting frame structures under post-mainshock cascading events

The paper presented herein proposes a reliability-based framework for quantifying the structural robustness considering the occurrence of a major earthquake (mainshock) and subsequent cascading hazard events, such as aftershocks that are triggered by the mainshock. These events can significantly increase the probability of failure of buildings, especially for structures that are damaged during the mainshock. The application of the proposed framework is exemplified through three numerical case studies. The case studies correspond to three SAC steel moment frame buildings of 3-, 9-, and 20- stories, which were designed to pre-Northridge codes and standards. Twodimensional nonlinear finite element models of the buildings are developed using the Open System for Earthquake Engineering Simulation framework (OpenSees), using a finite-length plastic hinge beam model and a bilinear constitutive law with deterioration, and are subjected to multiple mainshock-aftershock seismic sequences. For the three buildings analyzed herein, it is shown that the structural reliability under a single seismic event can be significantly different from that under a sequence of seismic events. The reliability-based robustness indicator used shows that the structural robustness is influenced by the extent by which a structure can distribute damage.

Joining copper to stainless steel by friction stir diffusion process

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do Grau de Mestre em Engenharia Mecânica

Development of ion jelly thin films for electrochemical devices

Dissertação para obtenção do Grau de Doutor em Química Sustentável