Scanning tunnelling microscopy observation of cytochrome-c denaturation induced by bromopyrogal red on highly oriented pyrolytic graphite

The denaturation of cytochrome-e (cyt-c) induced by bromopyrogal red (BPR) was studied by scanning tunnelling microscopy (STM) on the electrochemically pretreated highly oriented pyrolytic graphite (HOPG) surface. STM images reveal that denatured cyt-c molecules exist in variable states including aggregates, globular compact, partially unfolded and combined with BPR molecule. The apparently low image contrast of denatured cyt-c observed in this experiment comparing to that of native cyt-c molecules, and the relative low image contrast of the unfolded part comparing with the compact globular part, are ascribed to the unfavourable tunnelling paths for the conformational variations of denatured cyt-c molecules. (C) 1997 Elsevier Science B.V.

Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging.

In most diffusion tensor imaging (DTI) studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI) sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR). However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact). Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact) associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2(∗) -weighting (i.e., Type 3 artifact). These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

Salinity-induced effects on transpiration rate, stomatal conductance and leaf area of three olive (Olea europaea L.) varieties

Transpiration of two year-old olive trees of three different varieties, Arbequina, Cobrançosa and Galega (18 trees per variety), irrigated with three levels of salt (0, 80 or 200 mM NaCl) for about 90 days, was measured by a gravimetric method. To determine leaf area, each tree was photographed from the side against a white background and the total area of each projected image was determined with ImageJ software. To calibrate these area determinations, one tree of each variety was subsequently stripped of all its leaves and its total leaf area was accurately measured. A correlation was then obtained between the area on the photograph of this particular tree and the total area of the detached leaves of the same tree. Using the leaf area determined by this procedure, transpiration rates of the trees could be calculated. Knowing leaf and air temperatures and RH, it was possible to determine the difference in molar fraction of water between the leaf and the air. Using this and the values of the transpiration rate, stomatal conductance could be calculated (gs calc) and compared with the conductance measured on the same trees with a porometer (gs). Actual leaf area of a plant was 1,40 (Arbequina), 1,42 (Cobrançosa) or 1,24 (Galega) times the area measured with ImageJ on the photograph of the same plant. Leaf area of the trees, on average of all salt irrigations, was significantly higher on Arbequina (0,187 m2) then on the other two varieties (0,138 m2 or 0,148 m2, for Cobrançosa or Galega, respectively), but did not differ significantly in percentage of controls (0 salt). On average of all three varieties, leaf area was also higher on plants irrigated without salt (0,181 m2) than on plants exposed to 80 or 200 mM NaCl (0,152 m2 or 0,140 m2, respectively), which did not differ between them. The same significant difference was observed when leaf area was expressed as percentage of controls. Transpiration rate was significantly higher on Cobrançosa (1,17 mmol m-2 s-1), on average of all treatments, but there were no significant differences between Arbequina (1,08 mmol m-2 s-1) and Galega (0,82 mmol m-2 s-1). In percentage of controls, there were no significant differences between varieties. Salt reduced significantly the transpiration rate in all varieties, both the actual and percentual values, to about 50% or 30% of controls when exposed to 80 mM or 200 mM NaCl, respectively. Stomatal conductance (gs), assessed by porometry, was significantly higher in control plants, mainly in Cobrançosa (102 mmol m-2 s-1), then in Arbequina (77 mmol m-2 s-1) and the lower values were found in Galega (51 mmol m-2 s-1). Salt reduced gs, on average of the three varieties to 30% or 10% of controls on exposure to 80 mM or 200 mM NaCl, respectively. Calculated (gs calc) and measured (gs) values of stomatal conductance showed a close relation between them (0,967, R2 = 0,837) which indicates this non-destructive method to determine whole-plant leaf area to be reasonably accurate.

Translating proteomics into environmental health : biomarkers discovery for tobacco smoke-induced biological damage

Tese de doutoramento, Biologia (Biologia Molecular), Universidade de Lisboa, Faculdade de Ciências, 2015

Confocal and two-photon microscopy : image enhancement /

Confocal and two-photon microcopy have become essential tools in biological research and today many investigations are not possible without their help. The valuable advantage that these two techniques offer is the ability of optical sectioning. Optical sectioning makes it possible to obtain 3D visuahzation of the structiu-es, and hence, valuable information of the structural relationships, the geometrical, and the morphological aspects of the specimen. The achievable lateral and axial resolutions by confocal and two-photon microscopy, similar to other optical imaging systems, are both defined by the diffraction theorem. Any aberration and imperfection present during the imaging results in broadening of the calculated theoretical resolution, blurring, geometrical distortions in the acquired images that interfere with the analysis of the structures, and lower the collected fluorescence from the specimen. The aberrations may have different causes and they can be classified by their sources such as specimen-induced aberrations, optics-induced aberrations, illumination aberrations, and misalignment aberrations. This thesis presents an investigation and study of image enhancement. The goal of this thesis was approached in two different directions. Initially, we investigated the sources of the imperfections. We propose methods to eliminate or minimize aberrations introduced during the image acquisition by optimizing the acquisition conditions. The impact on the resolution as a result of using a coverslip the thickness of which is mismatched with the one that the objective lens is designed for was shown and a novel technique was introduced in order to define the proper value on the correction collar of the lens. The amoimt of spherical aberration with regard to t he numerical aperture of the objective lens was investigated and it was shown that, based on the purpose of our imaging tasks, different numerical apertures must be used. The deformed beam cross section of the single-photon excitation source was corrected and the enhancement of the resolution and image quaUty was shown. Furthermore, the dependency of the scattered light on the excitation wavelength was shown empirically. In the second part, we continued the study of the image enhancement process by deconvolution techniques. Although deconvolution algorithms are used widely to improve the quality of the images, how well a deconvolution algorithm responds highly depends on the point spread function (PSF) of the imaging system applied to the algorithm and the level of its accuracy. We investigated approaches that can be done in order to obtain more precise PSF. Novel methods to improve the pattern of the PSF and reduce the noise are proposed. Furthermore, multiple soiu'ces to extract the PSFs of the imaging system are introduced and the empirical deconvolution results by using each of these PSFs are compared together. The results confirm that a greater improvement attained by applying the in situ PSF during the deconvolution process.

Clustering algorithms and shape factor methods to discriminate among small GTPase phenotypes using DIC image analysis.

Naïvement perçu, le processus d’évolution est une succession d’événements de duplication et de mutations graduelles dans le génome qui mènent à des changements dans les fonctions et les interactions du protéome. La famille des hydrolases de guanosine triphosphate (GTPases) similaire à Ras constitue un bon modèle de travail afin de comprendre ce phénomène fondamental, car cette famille de protéines contient un nombre limité d’éléments qui diffèrent en fonctionnalité et en interactions. Globalement, nous désirons comprendre comment les mutations singulières au niveau des GTPases affectent la morphologie des cellules ainsi que leur degré d’impact sur les populations asynchrones. Mon travail de maîtrise vise à classifier de manière significative différents phénotypes de la levure Saccaromyces cerevisiae via l’analyse de plusieurs critères morphologiques de souches exprimant des GTPases mutées et natives. Notre approche à base de microscopie et d’analyses bioinformatique des images DIC (microscopie d’interférence différentielle de contraste) permet de distinguer les phénotypes propres aux cellules natives et aux mutants. L’emploi de cette méthode a permis une détection automatisée et une caractérisation des phénotypes mutants associés à la sur-expression de GTPases constitutivement actives. Les mutants de GTPases constitutivement actifs Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V ont été analysés avec succès. En effet, l’implémentation de différents algorithmes de partitionnement, permet d’analyser des données qui combinent les mesures morphologiques de population native et mutantes. Nos résultats démontrent que l’algorithme Fuzzy C-Means performe un partitionnement efficace des cellules natives ou mutantes, où les différents types de cellules sont classifiés en fonction de plusieurs facteurs de formes cellulaires obtenus à partir des images DIC. Cette analyse démontre que les mutations Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V induisent respectivement des phénotypes amorphe, allongé, rond et large qui sont représentés par des vecteurs de facteurs de forme distincts. Ces distinctions sont observées avec différentes proportions (morphologie mutante / morphologie native) dans les populations de mutants. Le développement de nouvelles méthodes automatisées d’analyse morphologique des cellules natives et mutantes s’avère extrêmement utile pour l’étude de la famille des GTPases ainsi que des résidus spécifiques qui dictent leurs fonctions et réseau d’interaction. Nous pouvons maintenant envisager de produire des mutants de GTPases qui inversent leur fonction en ciblant des résidus divergents. La substitution fonctionnelle est ensuite détectée au niveau morphologique grâce à notre nouvelle stratégie quantitative. Ce type d’analyse peut également être transposé à d’autres familles de protéines et contribuer de manière significative au domaine de la biologie évolutive.

Swift heavy ion induced surface and microstructural evolution in metallic glass thin films

Swift heavy ion induced changes in microstructure and surface morphology of vapor deposited Fe–Ni based metallic glass thin films have been investigated by using atomic force microscopy, X-ray diffraction and transmission electron microscopy. Ion beam irradiation was carried out at room temperature with 103 MeV Au9+ beam with fluences ranging from 3 1011 to 3 1013 ions/cm2. The atomic force microscopy images were subjected to power spectral density analysis and roughness analysis using an image analysis software. Clusters were found in the image of as-deposited samples, which indicates that the film growth is dominated by the island growth mode. As-deposited films were amorphous as evidenced from X-ray diffraction; however, high resolution transmission electron microscopy measurements revealed a short range atomic order in the samples with crystallites of size around 3 nm embedded in an amorphous matrix. X-ray diffraction pattern of the as-deposited films after irradiation does not show any appreciable changes, indicating that the passage of swift heavy ions stabilizes the short range atomic ordering, or even creates further amorphization. The crystallinity of the as-deposited Fe–Ni based films was improved by thermal annealing, and diffraction results indicated that ion beam irradiation on annealed samples results in grain fragmentation. On bombarding annealed films, the surface roughness of the films decreased initially, then, at higher fluences it increased. The observed change in surface morphology of the irradiated films is attributed to the interplay between ion induced sputtering, volume diffusion and surface diffusion

Magnetic and topographical modifications of amorphous Co–Fe thin films induced by high energy Ag7+ ion irradiation

We have investigated the effects of swift heavy ion irradiation on thermally evaporated 44 nm thick, amorphous Co77Fe23 thin films on silicon substrates using 100 MeV Ag7+ ions fluences of 1 1011 ions/ cm2, 1 1012 ions/cm2, 1 1013 ions/cm2, and 3 1013 ions/cm2. The structural modifications upon swift heavy irradiation were investigated using glancing angle X-ray diffraction. The surface morphological evolution of thin film with irradiation was studied using Atomic Force Microscopy. Power spectral density analysis was used to correlate the roughness variation with structural modifications investigated using X-ray diffraction. Magnetic measurements were carried out using vibrating sample magnetometry and the observed variation in coercivity of the irradiated films is explained on the basis of stress relaxation. Magnetic force microscopy images are subjected to analysis using the scanning probe image processor software. These results are in agreement with the results obtained using vibrating sample magnetometry. The magnetic and structural properties are correlated

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye and analysed by two-dimensional difference gel electrophoresis. Gel images analysed off-line, using the DeCyder image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Sample-induced beam distortions in terahertz time domain spectroscopy and imaging systems

It is demonstrated that distortion of the terahertz beam profile and generation of a cross-polarised component occur when the beam in terahertz time domain spectroscopy and imaging systems interacts with the sample under test. These distortions modify the detected signal, leading to spectral and image artefacts. The degree of distortion depends on the optical design of the system as well as the properties of the sample.

Evaluation of positioning error-induced pixel shifts on satellite linear push-broom imagery

Georeferencing is one of the major tasks of satellite-borne remote sensing. Compared to traditional indirect methods, direct georeferencing through a Global Positioning System/inertial navigation system requires fewer and simpler steps to obtain exterior orientation parameters of remotely sensed images. However, the pixel shift caused by geographic positioning error, which is generally derived from boresight angle as well as terrain topography variation, can have a great impact on the precision of georeferencing. The distribution of pixel shifts introduced by the positioning error on a satellite linear push-broom image is quantitatively analyzed. We use the variation of the object space coordinate to simulate different kinds of positioning errors and terrain topography. Then a total differential method was applied to establish a rigorous sensor model in order to mathematically obtain the relationship between pixel shift and positioning error. Finally, two simulation experiments are conducted using the imaging parameters of Chang’ E-1 satellite to evaluate two different kinds of positioning errors. The experimental results have shown that with the experimental parameters, the maximum pixel shift could reach 1.74 pixels. The proposed approach can be extended to a generic application for imaging error modeling in remote sensing with terrain variation.

Evaluation of curcumin and cisplatin-induced DNA damage in PC12 cells by the alkaline comet assay

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Pancreas Transplantation Prevents Morphologic and Ultrastructural Changes in Pulmonary Parenchyma of Alloxan-Induced Diabetic Rats

Purpose. The aim of this study was to evaluate whether pancreas transplantation (PT) is a suitable method for controlling histopathologic changes in lungs of alloxan-induced diabetic rats.Methods. Sixty inbred male Lewis rats were randomly assigned to 3 experimental groups: NC, 20 nondiabetic control rats; DC, 20 untreated diabetic control rats; and PT, 20 diabetic rats that received syngeneic PT from normal donor Lewis rats. Each group was further divided into 2 subgroups of 10 rats each, which were killed after 4 and 12 weeks of follow-up. Clinical and laboratory parameters, fresh and fixed lung weights, and fixed lung volumes were recorded for all rats. Total number of alveoli, alveolar perimeter, alveolar surface area, and alveolar epithelial (AE) and endothelial capillary (EC) basal laminae thickening were randomly measured in 5 rats from each subgroup by using an image analyzer. For light microscopy, 250 alveoli were analyzed in each subgroup. For electron microscopy, 50 electron micrographs were examined for each subgroup.Results. The DC rats showed elevated blood glucose and glycosylated hemoglobin levels, with insulin blood levels significantly lower than the NC rats (P < .001). Fresh and fixed lung weights and fixed volumes were significantly reduced in these rats, although their proportions to body weight were increased at 12 weeks (P < .01). The total number of alveoli in diabetic rats was higher than in control rats, whereas alveolar perimeter and surface area were significantly diminished (P < .01). AE and EC basal laminae were significantly thicker in DC than in NC (P < .01). Successful PT corrected all clinical and metabolic changes in diabetic rats, with sustained normoglycemia throughout the study. Morphologic and morphometric changes observed in diabetic lungs were completely prevented in PT rats from 4 weeks after transplant.Conclusion. We conclude that PT can control morphologic and ultrastructural changes in pulmonary parenchyma, suggesting a promising perspective for preventing other chronic diabetic lesions.

Histopathologic Changes Induced by Intense Pulsed Light in the Treatment of Poikiloderma of Civatte

Background The clinical efficacy of intense pulsed light (IPL) in the treatment of poikiloderma of Civatte (PC) is well documented, but little is known about microscopic changes. Objective To analyze histopathologic findings on the necks of individuals with PC after IPL therapy. Materials and Methods Fourteen patients with PC on the neck underwent three monthly sessions of IPL. Biopsies and clinical photographs were taken before and 60 similar to days after treatment. A dermatopathologist analyzed histopathologic slides stained with hematoxylin and eosin, Masson's trichrome, Verhoeff-van Gieson and Fontana-Masson or processed for CD-34 immunohistochemistry. The slides also underwent digital image analysis. Clinical results were based on the analysis of the pictures by three dermatologists and on patient satisfaction. Results Intense pulsed light treatment resulted in more-homogeneous melanin distribution; a greater number of fibroblasts and nonfragmented elastic fibers; and greater density (p similar to=similar to.01), color intensity (p similar to=similar to.02), number and thickness of the collagen bundles. No significant changes in vessels number or diameters were observed. Clinical results were positive in 92.9% of the cases. Conclusion IPL treatment of PC induced a more-homogeneous distribution of melanin and increased nonfragmented elastic fibers, collagen density, and intensity. These changes were related to clinical improvement.