Development of new methodologies in sample treatment for proteomics workflow based on enzymatic probe sonication technology and mass spectrometry

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia, for the degree of Doctor of Philosophy in Biochemistry

Heat stress adaptation in hyperthermophiles: bosynthesis of inositol-containing compatible solutes

Dissertation presented to obtain the Ph.D. degree in Biochemistry

Disposable solid state probe for optical screening of chlorpromazine

We are presenting a simple, low-cost and rapid solid-state optical probe for screening chlorpromazine (CPZ) in aquacultures. The method exploits the colourimetric reaction between CPZ and Fe(III) ion that occurs at a solid/liquid interface, the solid layer consisting of ferric iron entrapped in a layer of plasticized PVC. If solutions containing CPZ are dropped onto such a layer, a colour change occurs from light yellow to dark pink or even light blue, depending on the concentration of CPZ. Visual inspection enables the concentration of CPZ to be estimated. The resulting colouration was also monitored by digital image collection for a more accurate quantification. The three coordinates of the hue, saturation and lightness system were obtained by standard image processing along with mathematical data treatment. The parameters affecting colour were assessed and optimized. Studies were conducted by visible spectrophotometry and digital image acquisition, respectively. The response of the optimized probe towards the concentration of CPZ was tested for several mathematical transformations of the colour coordinates, and a linear relation was found for the sum of hue and luminosity. The limit of detection is 50 μM (corresponding to about 16 μg per mL). The probe enables quick screening for CPZ in real water samples with prior sample treatment.

Quantification and viability analyses of Pseudokirchneriella subcapitata algal cells using image-based cytometry

This work aims to evaluate the feasibility of using image-based cytometry (IBC) in the analysis of algal cell quantification and viability, using Pseudokirchneriella subcapitata as a cell model. Cell concentration was determined by IBC to be in a linear range between 1 × 105 and 8 × 106 cells mL−1. Algal viability was defined on the basis that the intact membrane of viable cells excludes the SYTOX Green (SG) probe. The disruption of membrane integrity represents irreversible damage and consequently results in cell death. Using IBC, we were able to successfully discriminate between live (SG-negative cells) and dead algal cells (heat-treated at 65 °C for 60 min; SG-positive cells). The observed viability of algal populations containing different proportions of killed cells was well correlated (R 2 = 0.994) with the theoretical viability. The validation of the use of this technology was carried out by exposing algal cells of P. subcapitata to a copper stress test for 96 h. IBC allowed us to follow the evolution of cell concentration and the viability of copper-exposed algal populations. This technology overcomes several main drawbacks usually associated with microscopy counting, such as labour-intensive experiments, tedious work and lack of the representativeness of the cell counting. In conclusion, IBC allowed a fast and automated determination of the total number of algal cells and allowed us to analyse viability. This technology can provide a useful tool for a wide variety of fields that utilise microalgae, such as the aquatic toxicology and biotechnology fields.

Differential Internalization of Amphotericin B - Conjugated Nanoparticles in Human Cells and the Expression of Heat Shock Protein 70

Although a variety of nanoparticles (NPs) functionalized with amphotericin B, an antifungal agent widely used in the clinic, have been studied in the last years their cytotoxicity profile remains elusive. Here we show that human endothelial cells take up high amounts of silica nanoparticles (SNPs) conjugated with amphotericin B (AmB) (SNP-AmB) (65.4 12.4 pg of Si per cell) through macropinocytosis while human fibroblasts internalize relatively low amounts (2.3 0.4 pg of Si per cell) because of their low capacity for macropinocytosis. We further show that concentrations of SNP-AmB and SNP up to 400 mg/mL do not substantially affect fibroblasts. In contrast, endothelial cells are sensitive to low concentrations of NPs (above 10 mg/mL), in particular to SNP-AmB. This is because of their capacity to internalize high concentration of NPs and high sensitivity of their membrane to the effects of AmB. Low-moderate concentrations of SNP-AmB (up to 100 mg/mL) induce the production of reactive oxygen species (ROS), LDH release, high expression of pro-inflammatory cytokines and chemokines (IL-8, IL-6, G-CSF, CCL4, IL-1b and CSF2) and high expression of heat shock proteins (HSPs) at gene and protein levels. High concentrations of SNP-AmB (above 100 ug/mL) disturb membrane integrity and kill rapidly human cells(60% after 5 h). This effect is higher in SNP-AmB than in SNP.

Deletions within COL11A1 in Type 2 Stickler Syndrome Detected by Multiplex Ligation - Syndrome Detected by Multiplex Ligation Dependent Probe Amplification (MLPA)

Background: COL11A1 is a large complex gene around 250 kb in length and consisting of 68 exons. Pathogenic mutations in the gene can result in Stickler syndrome, Marshall syndrome or Fibrochondrogenesis. Many of the mutations resulting in either Stickler or Marshall syndrome alter splice sites and result in exon skipping, which because of the exon structure of collagen genes usually leaves the message in-frame. The mutant protein then exerts a dominant negative effect as it co-assembles with other collagen gene products. To date only one large deletion of 40 kb in the COL11A1, which was detected by RT-PCR, has been characterized. However, commonly used screening protocols, utilizing genomic amplification and exon sequencing, are unlikely to detect such large deletions. Consequently the frequency of this type of mutation is unknown. Case presentations: We have used Multiplex Ligation-Dependent Probe Amplification (MLPA) in conjunction with exon amplification and sequencing, to analyze patients with clinical features of Stickler syndrome, and have detected six novel deletions that were not found by exon sequencing alone. Conclusion: Exon deletions appear to represent a significant proportion of type 2 Stickler syndrome. This observation was previously unknown and so diagnostic screening of COL11A1 should include assays capable of detecting both large and small deletions, in addition to exon sequencing.

Heat recovery from wastewater: numerical modelling of sewer systems

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente, perfil Engenharia Sanitária

DIARRHEA OUTBREAK IN PERNAMBUCO, BRAZIL, ASSOCIATED WITH A HEAT-STABLE CYTOTOXIC ENTEROTOXIN PRODUCED BY Aeromonas caviae

SUMMARY In the present study enterotoxic and cytotoxic activities of twenty Aeromonas caviaestrains were examined. They originated from fecal specimens of patients with acute diarrhea during an outbreak in Brazil in 2004. Culture supernatants of fourteen strains (70%) caused fluid accumulation in rabbit ileal intestinal loops and in suckling mice assays, and also showed a cytotoxic activity in Vero and Caco-2 cells. The enterotoxic and cytotoxic factors were heat-stable after culture supernatants treatment at 100 ºC. The results revealed that A. caviaestrains produce a putative diarrheagenic virulence factor, a heat-stable cytotoxic enterotoxin that could be linked to the diarrhea outbreak that took place in Brazil.

Target-specific multiphysics modeling for thermal medicine applications

Dissertation to obtain the degree of Doctor of Philosophy in Biomedical Engineering

Characterization of processed materials by electrical currents: development of equipment and applications

Dissertação para obtenção do Grau de Mestre em Engenharia Mecânica

Digoxigenin-labeled probe for rabies virus nucleoprotein gene detection

A digoxigenin-labeled probe was produced from the Pasteur virus strain for the detection of the rabies virus N gene. The probe hybridization was performed from amplified N gene obtained by reverse transcription polymerase chain reaction and the results by RT-PCR and hybridization showed 100% agreement. The hybridization, when carried out in products amplified by RT-PCR, increases the sensitivity of this technique even more and confers specificity to the diagnosis. The technique described in this work will be useful in rabies diagnosis laboratories, once the cost is compatible with traditional rabies diagnostic techniques.

Lime mortars with heat treated clays and ceramic waste: A review

The formulation and use of lime mortars with ceramic particles has, in the past, been a very common technique. Knowledge of such used techniques and materials is fundamental for the successful rehabilitation and conservation of the built heritage. The durability that these mortars have shown encourages the study of the involved mechanisms, so that they may be adapted to the current reality. The considerable amount of waste from old ceramics factories which is sent for disposal might present an opportunity for the production of reliable improved lime mortars. In this paper a number of studies that characterize old building mortars containing ceramic fragments are reviewed. The most important research undertaken on laboratory prepared mortars with several heat treated clays types is presented, specifically with incorporated ceramic waste. Some studies on the pozzolanicity of heat treated clays are examined and the heating temperatures that seem most likely to achieve pozzolanicity are presented. It was verified that some heating temperatures currently used by ceramic industries might correspond to the temperatures that will achieve pozzolanicity.

Gas gap heat switch for CryoFree project

Cryogen-free superconducting magnet systems have become popular during the last two decades for the simple reason that with the use of liquid helium is rather cumbersome and is a scarce resource. Some available CFMS uses a mechanical cryocooler as cold source of the superconductor magnet. However, the cooling of the sample holder is still made through an open circuit of helium. A thermal management of a completely cryogen-free system is possible to be implemented by using a controlled gas gap heat switch (GGHS) between the cryocooler and the variable temperature insert (VTI). This way it would eliminate the helium open circuit. Heat switches are devices that allow to toggle between two distinct thermal states (ON and OFF state). Several cryogenic applications need good thermal contact and a good thermal insulation at different stages of operation. A versatile GGHS was designed and built with a 100 mm gap and tested with helium as exchange gas. An analytic thermal model was developed and a good agreement with the experimental data was obtained. The device was tested on a crycooler at 4 to 80 K ranges. A 285 mW/K thermal conductance was measured at ON state and 0.09 mW/K at OFF. 3000 ON/OFF thermal conductance ratio was obtained at 4 K with helium.

Functional genomic analysis of heat stress in Vitis vinifera

Grapevine (Vitis vinifera) is one of most agro-economically important fruit crops worldwide, with a special relevance in Portugal where over 300 varieties are used for wine production. Due to global warming, temperature stress is currently a serious issue affecting crop production especially in temperate climates. Mobile genetic elements such as retrotransposons have been shown to be involved in environmental stress induced genetic and epigenetic modifications. In this study, sequences related to Grapevine Retrotransposon 1 (Gret1) were utilized to determine heat induced genomic and transcriptomic modifications in Touriga Nacional, a traditional Portuguese grapevine variety. For this purpose, growing canes were treated to 42 oC for four hours and leaf genomic DNA and RNA was utilized for various techniques to observe possible genomic alterations and variation in transcription levels of coding and non-coding sequences between non-treated plants and treated plants immediately after heat stress (HS-0 h) or after a 24 hour recovery period (HS-24 h). Heat stress was found to induce a significant decrease in Gret1 related sequences in HS-24 h leaves, indicating an effect of heat stress on genomic structure. In order to identify putative heat induced DNA modifications, genome wide approaches such as Amplified Fragment Length Polymorphism were utilized. This resulted in the identification of a polymorphic DNA fragment in HS-0 h and HS-24 h leaves whose sequence mapped to a genomic region flanking a house keeping gene (NADH) that is represented in multiple copies in the Vitis vinifera genome. Heat stress was also found to affect the transcript levels of various non-coding and gene coding sequences. Accordingly, quantitative real time PCR results established that Gret1 related sequences are up regulated immediately after heat stress whereas the level of transcript of genes involved in identification and repair of double strand breaks are significantly down regulated in HS-0 h plants. Taken together, the results of this work demonstrated heat stress affects both genomic integrity and transcription levels.

Insights into the biochemical strategies of adaptation to heat stress in the hyperthermophilic archaeon Pyrococcus furiosus

Organisms that thrive optimally at temperatures above 80°C are called hyperthermophiles. These prokaryotes have been isolated from a variety of hot environments, such as marine geothermal areas, hence they are usually slightly halophilic. Like other halophiles, marine hyperthermophiles have to cope with fluctuations in the salinity of the external medium and generally use low-molecular mass organic compounds to adjust cell turgor pressure. These compounds can accumulate to high levels without interfering with cell metabolism, thereby deserving the designation of compatible solutes. Curiously, the accumulation of compatible solutes also occurs in response to supraoptimal temperatures.(...)