Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences

Nucleic acids play key roles in the storage and processing of genetic information, as well as in the regulation of cellular processes. Consequently, they represent attractive targets for drugs against gene-related diseases. On the other hand, synthetic oligonucleotide analogues have found application as chemotherapeutic agents targeting cellular DNA and RNA. The development of effective nucleic acid-based chemotherapeutic strategies requires adequate analytical techniques capable of providing detailed information about the nucleotide sequences, the presence of structural modifications, the formation of higher-order structures, as well as the interaction of nucleic acids with other cellular components and chemotherapeutic agents. Due to the impressive technical and methodological developments of the past years, tandem mass spectrometry has evolved to one of the most powerful tools supporting research related to nucleic acids. This review covers the literature of the past decade devoted to the tandem mass spectrometric investigation of nucleic acids, with the main focus on the fundamental mechanistic aspects governing the gas-phase dissociation of DNA, RNA, modified oligonucleotide analogues, and their adducts with metal ions. Additionally, recent findings on the elucidation of nucleic acid higher-order structures by tandem mass spectrometry are reviewed.

Effects of incomplete combustion on atmospheric chemistry: Black carbon climate forcing and global carbon monoxide emissions

This thesis is actually the composition of two separate studies aimed at further understanding the role of incomplete combustion products on atmospheric chemistry. The first explores the sensitivity of black carbon (BC) forcing to aerosol vertical location since BC has an increased forcing per unit mass when it is located above reflective clouds. We used a column radiative transfer model to produce globally-averaged values of normalized direct radiative forcing (NDRF) for BC over and under different types of clouds. We developed a simple column-weighting scheme based on the mass fractions of BC that are over and under clouds in measured vertical profiles. The resulting NDRF is in good agreement with global 3-D model estimates, supporting the column-weighted model as a tool for exploring uncertainties due to diversity in vertical distribution. BC above low clouds accounts for about 20% of the global burden but 50% of the forcing. We estimate maximum-minimum spread in NDRF due to modeled profiles as about 40% and uncertainty as about 25%. Models overestimate BC in the upper troposphere compared with measurements; modeled NDRF might need to be reduced by about 15%. Redistributing BC within the lowest 4 km of the atmosphere affects modeled NDRF by only about 5% and cannot account for very high forcing estimates. The second study estimated global year 2000 carbon monoxide (CO) emissions using a traditional bottom-up inventory. We applied literature-derived emission factors to a variety of fuel and technology combinations. Combining these with regional fuel use and production data we produced CO emissions estimates that were separable by sector, fuel type, technology, and region. We estimated year 2000 stationary source emissions of 685.9 Tg/yr and 885 Tg/yr if we included adopted mobile sources from EDGAR v3.2FT2000. Open/biomass burning contributed most significantly to global CO burden, while the residential sector, primarily in Asia and Africa, were the largest contributors with respect to contained combustion sources. Industry production in Asia, including brick, cement, iron and steel-making, also contributed significantly to CO emissions. Our estimates of biofuel emissions are lower than most previously published bottom-up estimates while our other fuel emissions are generally in good agreement. Our values are also universally lower than recently estimated CO emissions from models using top-down methods.

Effect of Inorganic and Organic Carbon Enrichments (DIC and DOC) on the Photosynthesis and Calcification Rates of Two Calcifying Green Algae from a Caribbean Reef Lagoon

Coral reefs worldwide are affected by increasing dissolved inorganic carbon (DIC) and organic carbon (DOC) concentrations due to ocean acidification (OA) and coastal eutrophication. These two stressors can occur simultaneously, particularly in near-shore reef environments with increasing anthropogenic pressure. However, experimental studies on how elevated DIC and DOC interact are scarce and fundamental to understanding potential synergistic effects and foreseeing future changes in coral reef function. Using an open mesocosm experiment, the present study investigated the impact of elevated DIC (pHNBS: 8.2 and 7.8; pCO2: 377 and 1076 μatm) and DOC (added as 833 μmol L-1 of glucose) on calcification and photosynthesis rates of two common calcifying green algae, Halimeda incrassata and Udotea flabellum, in a shallow reef environment. Our results revealed that under elevated DIC, algal photosynthesis decreased similarly for both species, but calcification was more affected in H. incrassata, which also showed carbonate dissolution rates. Elevated DOC reduced photosynthesis and calcification rates in H. incrassata, while in U. flabellum photosynthesis was unaffected and thalus calcification was severely impaired. The combined treatment showed an antagonistic effect of elevated DIC and DOC on the photosynthesis and calcification rates of H. incrassata, and an additive effect in U. flabellum. We conclude that the dominant sand dweller H. incrassata is more negatively affected by both DIC and DOC enrichments, but that their impact could be mitigated when they occur simultaneously. In contrast, U. flabellum can be less affected in coastal eutrophic waters by elevated DIC, but its contribution to reef carbonate sediment production could be further reduced. Accordingly, while the capacity of environmental eutrophication to exacerbate the impact of OA on algal-derived carbonate sand production seems to be species-specific, significant reductions can be expected under future OA scenarios, with important consequences for beach erosion and coastal sediment dynamics.

Carbon gold rush and carbon cowboys: a new chapter in green mythology?

Individual and collective efforts to mitigate climate change in the form of carbon offsetting and emissions trading schemes have recently become the focus of much media attention. In this paper we explore a subset of the UK national press coverage centered on such schemes. The articles, selected from general as well as specialized business and finance newspapers, make use of gold rush, Wild West and cowboy imagery which is rooted in deeply entrenched myths and metaphors and allows readers to make sense of very complex environmental, political, ethical, and financial issues associated with carbon mitigation. They make what appears complicated and unfamiliar, namely carbon trading and offsetting, seem less complex and more familiar. A critical discussion of this type of imagery is necessary in order to uncover and question tacit assumptions and connotations which are built into it and which might otherwise go unnoticed and unchallenged in environmental communication.

Mesoporous Carbon as effective and sustainable catalyst for fine chemistry

It is well known that activated carbon with welldeveloped porosity is a promising material that have been used for several applications, from adsorption to catalysis. Research in this field has intensified in recent years, looking for new and improved characteristics and applications. Our research group, recently renamed Materials for Adsorption and Catalysis group (MAC) in LAQV-REQUIMTE, has also devoted many research work in this subject, and has developed several collaboration works with other national and international research groups in the field. Among our research group interests there is the study of catalytic properties of carbon materials and specifically mesoporous carbon. Some of the promising results were selected and summarized here, demonstrating that mesoporous carbon is an efficient and environmentally friendly heterogeneous catalyst.

Multi-organ support device for combined extracorporeal carbon dioxide removal and hemofiltration treatments with pump-free solution for ultrafiltration

The use of extracorporeal organ support (ECOS) devices is increasingly widespread, to temporarily sustain or replace the functions of impaired organs in critically ill patients. Among ECOS, respiratory functions are supplied by extracorporeal life support (ECLS) therapies like extracorporeal membrane oxygenation (ECMO) and extracorporeal carbon dioxide removal (ECCO2R), and renal replacement therapies (RRT) are used to support kidney functions. However, the leading cause of mortality in critically ill patients is multi-organ dysfunction syndrome (MODS), which requires a complex therapeutic strategy where extracorporeal treatments are often integrated to pharmacological approach. Recently, the concept of multi-organ support therapy (MOST) has been introduced, and several forms of isolated ECOS devices are sequentially connected to provide simultaneous support to different organ systems. The future of critical illness goes towards the development of extracorporeal devices offering multiple organ support therapies on demand by a single hardware platform, where treatment lines can be used alternately or in conjunction. The aim of this industrial PhD project is to design and validate a device for multi-organ support, developing an auxiliary line for renal replacement therapy (hemofiltration) to be integrated on a platform for ECCO2R. The intended purpose of the ancillary line, which can be connected on demand, is to remove excess fluids by ultrafiltration and achieve volume control by the infusion of a replacement solution, as patients undergoing respiratory support are particularly prone to develop fluid overload. Furthermore, an ultrafiltration regulation system shall be developed using a powered and software-modulated pinch-valve on the effluent line of the hemofilter, proposed as an alternative to the state-of-the-art solution with peristaltic pump.

Photoacoustic investigations on the photostability of Coumarin 540-doped PMMA

In this paper, we present a laser-induced photoacoustic study on the photostability of laser dye Coumarin 540 doped in PMMA matrix and modified by the incorporation of low-molecular weight additives. The dependence of photostability of the dye on various experimental conditions, such as nature of solvents, incident optical power and dye concentration, is investigated in detail. The activation rates for the bleaching process are calculated for different concentrations and they suggest the possibility of two distinct mechanisms responsible for photodegradation. Further, analysis of the data confirms the linear dependence of photodegradation on the intensity of incident radiation. The role of different externally influencing parameters, such as wavelength and modulation frequency of incident radiation, is also discussed.

Propriedades de materiais nanoestruturados do sistema epoxídico DGEBA/TETA modificado com um éster de silsesquioxano

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)