Bilipid membrane phase characterization by reflectance anisotropy spectroscopy (RAS)

In this work we propose the use of experimental and theoretical reflectance anisotropy spectra (RAS) as a new tool to identify structural and dynamical aspects of the bilipid membrane and its various constituent molecules. The role of geometric details at the atomic level and macroscopic quantities, such as the membrane curvature and tilt for the different gel phases, in the theoretical RAS spectra (using Kohn-Sham density functional theory (KS-DFT)) are presented. Then the results are compared to the experimentally measured spectra taken from other techniques.

Positron annihilation spectroscopy techniques applied to the study of an HPGe detector.

Doppler Broadening Spectroscopy of the large Ge crystal of an HPGe detector was perforrned using positrons from pair production of 6.13 MeV ϒ-rays from the 19F(p,αϒ) 16O reaction. Two HPGe detectors facing opposite sides of the Ge crystal acting as target provided both coincidence and singles spectra. Changes in the shape of the annihilation peak were observed when the high voltage applied to the target detector was switched on or off, amounting to somewhat less than 20% when the areas of equivalent energy intervals in the corresponding normalized spectra are compared.

Bilipid Membrane Phase Characterization by Reflectance Anisotropy Spectroscopy (RAS)

In this work we propose the use of experimental and theoretical reflectance anisotropy spectra (RAS) as a new tool to identify structural and dynamical aspects of the bilipid membrane and its various constituent molecules. The role of geometric details at the atomic level and macroscopic quantities, such as the membrane curvature and tilt for the different gel phases, in the theoretical RAS spectra (using Kohn-Sham density functional theory (KS-DFT)) are presented. Then the results are compared to the experimentally measured spectra taken from other techniques.

História da propagação das citações originais do artigo do Journal of Quantitative Spectroscopy & Radiative Transfer 102/441/2006.

Neste artigo procuraremos descrever a história cronológica das citações originais (aquelas que os nomes dos autores aparecem apenas uma vez, portanto, excluídas as autocitações) da publicação do artigo: M. Cattani and J. M. F. Bassalo, Racemization, Chiral Stability and Weak Interactions, Journal of Quantitative Spectroscopy & Radiative Transfer 102, pp. 441-449, 2006 (CB: JQS&RT 102/441/2006). Para realizar essa história, usamos a WEB OF SCIENCE (acessado: 08/02/2013) disponibilizado pela CAPES/UFPA.

Determination of degree of ionization of poly(allylamine hydrochloride) (PAH) and poly[1-[4-(3-carboxy‑4 hydroxyphenylazo)benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) in layer-by-layer films using vacuum photoabsorption spectroscopy

Electrostatic and hydrophobic interactions govern most of the properties of supramolecular systems, which is the reason determining the degree of ionization of macromolecules has become crucial for many applications. In this paper, we show that highresolution ultraviolet spectroscopy (VUV) can be used to determine the degree of ionization and its effect on the electronic excitation energies of layer-by-layer (LbL) films of poly(allylamine hydrochloride) (PAH) and poly[1-[4-(3-carboxy-4 hydroxyphenylazo)- benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO). A full assignment of the VUV peaks of these polyelectrolytes in solution and in cast or LbL films could be made, with their pH dependence allowing us to determine the p'K IND. a' using the Henderson-Hasselbach equation. The p'K IND. a' for PAZO increased from ca. 6 in solution to ca. 7.3 in LbL films owing to the charge transfer from PAH. Significantly, even using solutions at a fixed pH for PAH, the amount adsorbed on the LbL films still varied with the pH of the PAZO solutions due to these molecular-level interactions. Therefore, the procedure based on a comparison of VUV spectra from solutions and films obtained under distinct conditions is useful to determine the degree of dissociation of macromolecules, in addition to permitting interrogation of interface effects in multilayer films.

Luminescence quantum efficiency at 1.5 µm of Er3+- doped tellurite glass determined by thermal lens spectroscopy

Erbium doped tellurite glasses (TeO2 + Li2O + TiO2) were prepared by conventional melt-quenching method to study the influence of the Er3+ concentration on the luminescence quantum efficiency (η) at 1.5 µm. Absorption and luminescence data were used to characterize the samples, and the η parameter was measured using the well-known thermal lens spectroscopy. For low Er3+ concentration, the measured values are around 76%, and the concentration behavior of η shows Er-Er and Er-OH- interactions, which agreed with the measured lifetime values.

Reaction intermediates of ethanol electro-oxidation on platinum investigated by SFG spectroscopy

Although electrochemical oxidation of simple organic molecules on metal catalysts is the basic ingredient of fuel cells, which have great technological potential as a renewable source of electrical energy, the detailed reaction mechanisms are in most cases not completely understood. Here, we investigate the ethanol-platinum interface in acidic aqueous solution using infrared-visible sum frequency generation (SFG) spectroscopy and theoretical calculations of vibrational spectra in order to identify the intermediates present during the electro-oxidation of ethanol. The complex vibrational spectrum in the fingerprint region imply on the coexistence of several adsorbates. Based on spectra in ultra-high-vacuum (UHV) and electrochemical environment from the literature and our density functional theory (DFT) calculations of vibrational spectra, new adsorbed intermediates, never before observed with conventional infrared (IR) spectroscopy, are proposed here: g2-acetaldehyde, g2-acetyl, ethylidyne, monodentate acetate, methoxy, tertiary methanol derivative, COH residue, g2-formaldehyde, mono and bidentate formate, CH3 and CH2 residues. In addition, we present new evidences for an ethoxy intermediate, a secondary ethanol derivative and an acetyl species, and we confirm the presence of previously observed adsorbates: a tertiary ethanol derivative, bidentate acetate, and COad. These results indicate that the platinum surface is much more reactive, and the reaction mechanism for ethanol electro-oxidation is considerably more complex than previously considered. This might be also true for many other molecule-catalyst systems.

ScPdZn and ScPtZn with YAlGe type structure: group-subgroup relation and 45Sc solid state NMR spectroscopy

The intermetallic compounds ScPdZn and ScPtZn were prepared from the elements by high-frequency melting in sealed tantalum ampoules. Both structures were refined from single crystal X-ray diffractometer data: YAlGe type, Cmcm, a = 429.53(8), b = 907.7(1), c = 527.86(1) pm, wR2 = 0.0375, 231 F2 values, for ScPdZn and a = 425.3(1), b = 918.4(2), c = 523.3(1) pm, wR2 = 0.0399, 213 F2 values for ScPtZn with 14 variables per refinement. The structures are orthorhombically distorted variants of the AlB2 type. The scandium and palladium (platinum atoms) build up ordered networks Sc3Pd3 and Sc3Pt3 (boron networks) which are slightly shifted with respect to each other. These networks are penetrated by chains of zinc atoms (262 pm in ScPtZn) which correspond to the aluminum positions, i.e. Zn(ScPd) and Zn(ScPt). The corresponding group-subgroup scheme and the differences in chemical bonding with respect to other AlB2-derived REPdZn and REPtZn compounds are discussed. 45Sc solid state NMR spectra confirm the single crystallographic scandium sites. From electronic band structure calculations the two compounds are found metallic with free electron like behavior at the Fermi level. A larger cohesive energy for ScPtZn suggests a more strongly bonded intermetallic than ScPdZn. Electron localization and overlap population analyses identify the largest bonding for scandium with the transition metal (Pd, Pt).

Structural and Interaction Studies of Bacterial Polysaccharides by NMR Spectroscopy

An introduction to bacterial polysaccharides and the methods for structural determination are described in the first two parts of the thesis. In a structural elucidation of bacterial polysaccharides NMR experiments are important as is component analysis. A short description of immunochemical methods such as enzyme immunoassays is included. Two NMR techniques used for interaction studies, trNOE and STD NMR, are also discussed. The third part of the thesis discusses and summarizes the results from the included papers. The structures of the exopolysaccharides produced by two lactic acid bacteria are determined by one- and two dimensional NMR experiments. One is a heteropolysaccharide produced by Streptococcus thermophilus and the other a homopolysaccharide produced by Propionibacterium freudenreichii. The structure of an acidic polysaccharide from a marine bacterium with two serine residues in the repeating unit is also investigated. The structural and immunological relationship between two O-antigenic polysaccharides from Escherichia coli strain 180/C3 and O5 is discussed and investigated. Finally, interaction studies of an octasaccharide derived from the Salmonella enteritidis O-antigen and a bacteriophage are described which were performed with NMR experiments.

Biochemistry in healthy and neoplastic human tissues: metabolic alteration revealed by HR-MAS nuclear magnetic resonance spectroscopy

This thesis is focused on the metabolomic study of human cancer tissues by ex vivo High Resolution-Magic Angle Spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy. This new technique allows for the acquisition of spectra directly on intact tissues (biopsy or surgery), and it has become very important for integrated metabonomics studies. The objective is to identify metabolites that can be used as markers for the discrimination of the different types of cancer, for the grading, and for the assessment of the evolution of the tumour. Furthermore, an attempt to recognize metabolites, that although involved in the metabolism of tumoral tissues in low concentration, can be important modulators of neoplastic proliferation, was performed. In addition, NMR data was integrated with statistical techniques in order to obtain semi-quantitative information about the metabolite markers. In the case of gliomas, the NMR study was correlated with gene expression of neoplastic tissues. Chapter 1 begins with a general description of a new “omics” study, the metabolomics. The study of metabolism can contribute significantly to biomedical research and, ultimately, to clinical medical practice. This rapidly developing discipline involves the study of the metabolome: the total repertoire of small molecules present in cells, tissues, organs, and biological fluids. Metabolomic approaches are becoming increasingly popular in disease diagnosis and will play an important role on improving our understanding of cancer mechanism. Chapter 2 addresses in more detail the basis of NMR Spectroscopy, presenting the new HR-MAS NMR tool, that is gaining importance in the examination of tumour tissues, and in the assessment of tumour grade. Some advanced chemometric methods were used in an attempt to enhance the interpretation and quantitative information of the HR-MAS NMR data are and presented in chapter 3. Chemometric methods seem to have a high potential in the study of human diseases, as it permits the extraction of new and relevant information from spectroscopic data, allowing a better interpretation of the results. Chapter 4 reports results obtained from HR-MAS NMR analyses performed on different brain tumours: medulloblastoma, meningioms and gliomas. The medulloblastoma study is a case report of primitive neuroectodermal tumor (PNET) localised in the cerebellar region by Magnetic Resonance Imaging (MRI) in a 3-year-old child. In vivo single voxel 1H MRS shows high specificity in detecting the main metabolic alterations in the primitive cerebellar lesion; which consist of very high amounts of the choline-containing compounds and of very low levels of creatine derivatives and N-acetylaspartate. Ex vivo HR-MAS NMR, performed at 9.4 Tesla on the neoplastic specimen collected during surgery, allows the unambiguous identification of several metabolites giving a more in-depth evaluation of the metabolic pattern of the lesion. The ex vivo HR-MAS NMR spectra show higher detail than that obtained in vivo. In addition, the spectroscopic data appear to correlate with some morphological features of the medulloblastoma. The present study shows that ex vivo HR-MAS 1H NMR is able to strongly improve the clinical possibility of in vivo MRS and can be used in conjunction with in vivo spectroscopy for clinical purposes. Three histological subtypes of meningiomas (meningothelial, fibrous and oncocytic) were analysed both by in vivo and ex vivo MRS experiments. The ex vivo HR-MAS investigations are very helpful for the assignment of the in vivo resonances of human meningiomas and for the validation of the quantification procedure of in vivo MR spectra. By using one- and two dimensional experiments, several metabolites in different histological subtypes of meningiomas, were identified. The spectroscopic data confirmed the presence of the typical metabolites of these benign neoplasms and, at the same time, that meningomas with different morphological characteristics have different metabolic profiles, particularly regarding macromolecules and lipids. The profile of total choline metabolites (tCho) and the expression of the Kennedy pathway genes in biopsies of human gliomas were also investigated using HR-MAS NMR, and microfluidic genomic cards. 1H HR-MAS spectra, allowed the resolution and relative quantification by LCModel of the resonances from choline (Cho), phosphorylcholine (PC) and glycerolphorylcholine (GPC), the three main components of the combined tCho peak observed in gliomas by in vivo 1H MRS spectroscopy. All glioma biopsies depicted an increase in tCho as calculated from the addition of Cho, PC and GPC HR-MAS resonances. However, the increase was constantly derived from augmented GPC in low grade NMR gliomas or increased PC content in the high grade gliomas, respectively. This circumstance allowed the unambiguous discrimination of high and low grade gliomas by 1H HR-MAS, which could not be achieved by calculating the tCho/Cr ratio commonly used by in vivo 1H MR spectroscopy. The expression of the genes involved in choline metabolism was investigated in the same biopsies. The present findings offer a convenient procedure to classify accurately glioma grade using 1H HR-MAS, providing in addition the genetic background for the alterations of choline metabolism observed in high and low gliomas grade. Chapter 5 reports the study on human gastrointestinal tract (stomach and colon) neoplasms. The human healthy gastric mucosa, and the characteristics of the biochemical profile of human gastric adenocarcinoma in comparison with that of healthy gastric mucosa were analyzed using ex vivo HR-MAS NMR. Healthy human mucosa is mainly characterized by the presence of small metabolites (more than 50 identified) and macromolecules. The adenocarcinoma spectra were dominated by the presence of signals due to triglycerides, that are usually very low in healthy gastric mucosa. The use of spin-echo experiments enable us to detect some metabolites in the unhealthy tissues and to determine their variation with respect to the healthy ones. Then, the ex vivo HR-MAS NMR analysis was applied to human gastric tissue, to obtain information on the molecular steps involved in the gastric carcinogenesis. A microscopic investigation was also carried out in order to identify and locate the lipids in the cellular and extra-cellular environments. Correlation of the morphological changes detected by transmission (TEM) and scanning (SEM) electron microscopy, with the metabolic profile of gastric mucosa in healthy, gastric atrophy autoimmune diseases (AAG), Helicobacter pylori-related gastritis and adenocarcinoma subjects, were obtained. These ultrastructural studies of AAG and gastric adenocarcinoma revealed lipid intra- and extra-cellularly accumulation associated with a severe prenecrotic hypoxia and mitochondrial degeneration. A deep insight into the metabolic profile of human healthy and neoplastic colon tissues was gained using ex vivo HR-MAS NMR spectroscopy in combination with multivariate methods: Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA). The NMR spectra of healthy tissues highlight different metabolic profiles with respect to those of neoplastic and microscopically normal colon specimens (these last obtained at least 15 cm far from the adenocarcinoma). Furthermore, metabolic variations are detected not only for neoplastic tissues with different histological diagnosis, but also for those classified identical by histological analysis. These findings suggest that the same subclass of colon carcinoma is characterized, at a certain degree, by metabolic heterogeneity. The statistical multivariate approach applied to the NMR data is crucial in order to find metabolic markers of the neoplastic state of colon tissues, and to correctly classify the samples. Significant different levels of choline containing compounds, taurine and myoinositol, were observed. Chapter 6 deals with the metabolic profile of normal and tumoral renal human tissues obtained by ex vivo HR-MAS NMR. The spectra of human normal cortex and medulla show the presence of differently distributed osmolytes as markers of physiological renal condition. The marked decrease or disappearance of these metabolites and the high lipid content (triglycerides and cholesteryl esters) is typical of clear cell renal carcinoma (RCC), while papillary RCC is characterized by the absence of lipids and very high amounts of taurine. This research is a contribution to the biochemical classification of renal neoplastic pathologies, especially for RCCs, which can be evaluated by in vivo MRS for clinical purposes. Moreover, these data help to gain a better knowledge of the molecular processes envolved in the onset of renal carcinogenesis.

Each one teaches one: characterizing active forms of proteins by single molecule force spectroscopy

This Ph.D. candidate thesis collects the research work I conducted under the supervision of Prof.Bruno Samor´ı in 2005,2006 and 2007. Some parts of this work included in the Part III have been begun by myself during my undergraduate thesis in the same laboratory and then completed during the initial part of my Ph.D. thesis: the whole results have been included for the sake of understanding and completeness. During my graduate studies I worked on two very different protein systems. The theorical trait d’union between these studies, at the biological level, is the acknowledgement that protein biophysical and structural studies must, in many cases, take into account the dynamical states of protein conformational equilibria and of local physico-chemical conditions where the system studied actually performs its function. This is introducted in the introductory part in Chapter 2. Two different examples of this are presented: the structural significance deriving from the action of mechanical forces in vivo (Chapter 3) and the complexity of conformational equilibria in intrinsically unstructured proteins and amyloid formation (Chapter 4). My experimental work investigated both these examples by using in both cases the single molecule force spectroscopy technique (described in Chapter 5 and Chapter 6). The work conducted on angiostatin focused on the characterization of the relationships between the mechanochemical properties and the mechanism of action of the angiostatin protein, and most importantly their intertwining with the further layer of complexity due to disulfide redox equilibria (Part III). These studies were accompanied concurrently by the elaboration of a theorical model for a novel signalling pathway that may be relevant in the extracellular space, detailed in Chapter 7.2. The work conducted on -synuclein (Part IV) instead brought a whole new twist to the single molecule force spectroscopy methodology, applying it as a structural technique to elucidate the conformational equilibria present in intrinsically unstructured proteins. These equilibria are of utmost interest from a biophysical point of view, but most importantly because of their direct relationship with amyloid aggregation and, consequently, the aetiology of relevant pathologies like Parkinson’s disease. The work characterized, for the first time, conformational equilibria in an intrinsically unstructured protein at the single molecule level and, again for the first time, identified a monomeric folded conformation that is correlated with conditions leading to -synuclein and, ultimately, Parkinson’s disease. Also, during the research work, I found myself in the need of a generalpurpose data analysis application for single molecule force spectroscopy data analysis that could solve some common logistic and data analysis problems that are common in this technique. I developed an application that addresses some of these problems, herein presented (Part V), and that aims to be publicly released soon.

Thermodynamic behavior of the binaries 1-butilpryridinium tetrafluoroborate with water and alkanols: their interpretation using 1H-NMR spectroscopy and quantum-chemistry calculations

[EN]Here we present experimental data of different properties for a set of binary mixtures composed of water or alkanols (methanol to butanol) with an ionic liquid (IL), butylpyridinium tetrafluoroborate [bpy][BF4]. Solubility data (xIL,T) are presented for each of the mixtures, including water, which is found to have a small interval of compositions in IL, xIL, with immiscibility. In each case, the upper critical solubility temperature (UCST) is determined and a correlation was observed between the UCST and the nature of the compounds in the mixtures. Miscibility curves establish the composition and temperature intervals where thermodynamic properties of the mixtures, such as enthalpies Hm E and volumes Vm E, can be determined.