Ankylosing spondylitis: genomic and functional characterization of candidate genes and their repercussion in clinical practice

RESUMO: Introdução: A espondilite anquilosante (EA) é uma doença inflamatória crónica caracterizada pela inflamação das articulações sacroilíacas e da coluna. A anquilose progressiva motiva uma deterioração gradual da função física e da qualidade de vida. O diagnóstico e o tratamento precoces podem contribuir para um melhor prognóstico. Neste contexto, a identificação de biomarcadores, assume-se como sendo muito útil para a prática clínica e representa hoje um grande desafio para a comunidade científica. Objetivos: Este estudo teve como objetivos: 1 - caracterizar a EA em Portugal; 2 - investigar possíveis associações entre genes, MHC e não-MHC, com a suscetibilidade e as características fenotípicas da EA; 3 - identificar genes candidatos associados a EA através da tecnologia de microarray. Material e Métodos: Foram recrutados doentes com EA, de acordo com os critérios modificados de Nova Iorque, nas consultas de Reumatologia dos diferentes hospitais participantes. Colecionaram-se dados demográficos, clínicos e radiológicos e colhidas amostras de sangue periférico. Selecionaram-se de forma aleatória, doentes HLA-B27 positivos, os quais foram tipados em termos de HLA classe I e II por PCR-rSSOP. Os haplótipos HLA estendidos foram estimados pelo algoritmo Expectation Maximization com recurso ao software Arlequin v3.11. As variantes alélicas dos genes IL23R, ERAP1 e ANKH foram estudadas através de ensaios de discriminação alélica TaqMan. A análise de associação foi realizada utilizando testes da Cochrane-Armitage e de regressão linear, tal como implementado pelo PLINK, para variáveis qualitativas e quantitativas, respetivamente. O estudo de expressão génica foi realizado por Illumina HT-12 Whole-Genome Expression BeadChips. Os genes candidatos foram validados usando qPCR-based TaqMan Low Density Arrays (TLDAs). Resultados: Foram incluídos 369 doentes (62,3% do sexo masculino, com idade média de 45,4 ± 13,2 anos, duração média da doença de 11,4 ± 10,5 anos). No momento da avaliação, 49,9% tinham doença axial, 2,4% periférica, 40,9% mista e 7,1% entesopática. A uveíte anterior aguda (33,6%) foi a manifestação extra-articular mais comum. Foram positivos para o HLA-B27, 80,3% dos doentes. Os haplótipo A*02/B*27/Cw*02/DRB1*01/DQB1*05 parece conferir suscetibilidade para a EA, e o A*02/B*27/Cw*01/DRB1*08/DQB1*04 parece conferir proteção em termos de atividade, repercussão funcional e radiológica da doença. Três variantes (2 para IL23R e 1 para ERAP1) mostraram significativa associação com a doença, confirmando a associação destes genes com a EA na população Portuguesa. O mesmo não se verificou com as variantes estudadas do ANKH. Não se verificou associação entre as variantes génicas não-MHC e as manifestações clínicas da EA. Foi identificado um perfil de expressão génica para a EA, tendo sido validados catorze genes - alguns têm um papel bem documentado em termos de inflamação, outros no metabolismo da cartilagem e do osso. Conclusões: Foi estabelecido um perfil demográfico e clínico dos doentes com EA em Portugal. A identificação de variantes génicas e de um perfil de expressão contribuem para uma melhor compreensão da sua fisiopatologia e podem ser úteis para estabelecer modelos com relevância em termos de diagnóstico, prognóstico e orientação terapêutica dos doentes. -----------ABSTRACT: Background: Ankylosing Spondylitis (AS) is a chronic inflammatory disorder characterized by inflammation in the spine and sacroiliac joints leading to progressive joint ankylosis and in progressive deterioration of physical function and quality of life. An early diagnosis and early therapy may contribute to a better prognosis. The identification of biomarkers would be helpful and represents a great challenge for the scientific community. Objectives: The present study had the following aims: 1- to characterize the pattern of AS in Portuguese patients; 2- to investigate MHC and non-MHC gene associations with susceptibility and phenotypic features of AS and; 3- to identify candidate genes associated with AS by means of whole-genome microarray. Material and Methods: AS was defined in accordance to the modified New York criteria and AS cases were recruited from hospital outcares patient clinics. Demographic and clinical data were recorded and blood samples collected. A random group of HLA-B27 positive patients and controls were selected and typed for HLA class I and II by PCR-rSSOP. The extended HLA haplotypes were estimated by Expectation Maximization Algorithm using Arlequin v3.11 software. Genotyping of IL23R, ERAP1 and ANKH allelic variants was carried out with TaqMan allelic discrimination assays. Association analysis was performed using the Cochrane-Armitage and linear regression tests as implemented in PLINK, for dichotomous and quantitative variables, respectively. Gene expression profile was carried out using Illumina HT-12 Whole-Genome Expression BeadChips and candidate genes were validated using qPCR-based TaqMan Low Density Arrays (TLDAs). Results: A total of 369 patients (62.3% male; mean age 45.4±13.2 years; mean disease duration 11.4±10.5 years), were included. Regarding clinical disease pattern, at the time of assessment, 49.9% had axial disease, 2.4% peripheral disease, 40.9% mixed disease and 7.1% isolated enthesopathic disease. Acute anterior uveitis (33.6%) was the most common extra-articular manifestation. 80.3% of AS patients were HLA-B27 positive. The haplotype A*02/B*27/Cw*02/DRB1*01/DQB1*05 seems to confer susceptibility to AS, whereas A*02/B*27/Cw*01/DRB1*08/DQB1*04 seems to provide protection in terms of disease activity, functional and radiological repercussion. Three markers (two for IL23R and one for ERAP1) showed significant single-locus disease associations. Association of these genes with AS in the Portuguese population was confirmed, whereas ANKH markers studied did not show an association with AS. No association was seen between non-MHC genes and clinical manifestations of AS. A gene expression signature for AS was established; among the fourteen validated genes, a number of them have a well-documented inflammatory role or in modulation of cartilage and bone metabolism. Conclusions: A demographic and clinical profile of patients with AS in Portugal was established. Identification of genetic variants of target genes as well as gene expression signatures could provide a better understanding of AS pathophysiology and could be useful to establish models with relevance in terms of susceptibility, prognosis, and potential therapeutic guidance.

Quantification and characterization of the phenolic compounds of kenaf leaves

Dissertation for the Master Degree in Technology and Food Security

The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774

Eur. J. Biochem. 270, 3904–3915 (2003)

Spectroscopic characterization of a novel 2 /[4Fe /4S] ferredoxin isolated from Desulfovibrio desulfuricans ATCC 27774

Inorganica Chimica Acta 356 (2003) 215-221

The transformation of work? A quantitative evaluation of changes in work in Portugal

This report is made for the Work Package 15 of WORKS project and tries to develop more information on the Portuguese situation in the work structures changes in the recent years. It starts with an analysis of socio- economical indicators (Macro economical indicators, Employment indicators, Consumption, Technology at the workplace, Productivity), and then approaches the situation in terms of work flexibility in its dimensions of time use and New forms of work organisation. It traces employment in business functions with a sectoral and occupational approach, and analyses the occupational change in South Europe with particular relevance to Portugal (skill utilisation and job satisfaction, occupational and industrial mobility, quantitative evaluation of the shape of employment in Europe. Finaly are analysed the globalisation indicators.

Synthesis, characterization and reactivity of new cobalt, palladium and nickel complexes bearing α-diimines and P, O ligands

This work describes the synthesis and characterization of a series of new α-diimine and P,O, β-keto and acetamide phosphines ligands, and their complexation to Ni(II), Co(II),Co(III) and Pd(II) to obtain a series of new compounds aiming to study their structural characteristics and to test their catalytic activity. All the compounds synthesized were characterized by the usual spectroscopic and spectrometric techniques: Elemental Analysis, MALDI-TOF-MS spectrometry, IR, UV-vis, 1H, 13C and 31P NMR spectroscopies. Some of the paramagnetic compounds were also characterized by EPR. For the majority of the compounds it was possible to solve their solid state structure by single crystal X-ray diffraction. Tests for olefin polymerization were performed in order to determine the catalytic activity of the Co(II) complexes. Chapter I presents a brief introduction to homogenous catalysis, highlighting the reactions catalyzed by the type of compounds described in this thesis, namely olefin polymerization and oligomerization and reactions catalyzed by the complexes bearing α-diimines and P,O type ligands. Chapter II is dedicated to the description of the synthesis of new α-diimines cobalt (II) complexes, of general formula [CoX2(α-diimine)], where X = Cl or I and the α-diimines are bis(aryl)acenaphthenequinonediimine) (Ar-BIAN) and 1,4-diaryl-2,3-dimethyl-1,4-diaza-1,3-butadiene (Ar-DAB). Structures solved by single crystal X-ray diffraction were obtained for all the described complexes. For some of the compounds, X-band EPR measurements were performed on polycrystalline samples, showing a high-spin Co(II) (S = 3/2) ion, in a distorted axial environment. EPR single crystal experiments on two of the compounds allowed us to determine the g tensor orientation in the molecular structure. In Chapter III we continue with the synthesis and characterization of more cobalt (II)complexes bearing α-diimines of general formula [CoX2(α-diimine)], with X = Cl or I and α-diimines are bis(aryl)acenaphthenequinonediimine) (Ar-BIAN) and 1,4-diaryl-2,3-dimethyl- 1,4-diaza-1,3-butadiene (Ar-DAB). The structures of three of the new compounds synthesized were determined by single crystal X-ray diffraction. A NMR paramagnetic characterization of all the compounds described is presented. Ethylene polymerization tests were done to determine the catalytic activity of several of the Co(II) complexes described in Chapter II and III and their results are shown. In Chapter IV a new rigid bidentate ligand, bis(1-naphthylimino)acenaphthene, and its complexes with Zn(II) and Pd(II), were synthesized. Both the ligand and its complexes show syn and anti isomers. Structures of the ligand and the anti isomer of the Pd(II) complex were solved by single crystal X-ray diffraction. All the compounds were characterized by elemental analysis, MALDI-TOF-MS spectrometry, and by IR, UV-vis, 1H, 13C, 1H-1H COSY, 1H-13C HSQC, 1H-13C HSQC-TOCSY and 1H-1H NOESY NMR when necessary. DFT studies showed that both conformers of [PdCl2(BIAN)] are isoenergetics and can be obtain experimentally. However, we can predict that the isomerization process is not available in square-planar complex, but is possible for the free ligand. The molecular geometry is very similar in both isomers, and only different orientations for naphthyl groups can be expected. Chapter V describes the synthesis of new P, O type ligands, β-keto phosphine, R2PCH2C(O)Ph, and acetamide phosphine R2PNHC(O)Me, as well as a series of new cobalt(III) complexes namely [(η5-C5H5)CoI2{Ph2PCH2C(O)Ph}], and [(η5- C5H5)CoI2{Ph2PNHC(O)Me}]. Treating these Co(III) compounds with an excess of Et3N, resulted in complexes η2-phosphinoenolate [(η5-C5H5)CoI{Ph2PCH…C(…O)Ph}] and η2- acetamide phosphine [(η5-C5H5)CoI{Ph2PN…C(…O)Me}]. Nickel (II) complexes were also obtained: cis-[Ni(Ph2PN…C(…O)Me)2] and cis-[Ni((i-Pr)2PN…C(…O)Me)2]. Their geometry and isomerism were discussed. Seven structures of the compounds described in this chapter were determined by single crystal X-ray diffraction. The general conclusions of this work can be found in Chapter VI.

Characterization and identification of printed objects

A study about the physical appearance of pre-photographic, photomechanical, photographic and digital positive reflective prints was made, relating the obtained images with the history, materials and technology used to create them. The studied samples are from the Image Permanence Institute (IPI) study collection. The digital images were obtained using a digital SLR on a copystand and a compound light microscope, with different lighting angles (0º, 45ºand 90º) and magnifications from overall views on the copystand down to a 20x objective lens on the microscope. Most of these images were originally created by IPI for www.digitalsamplebook.org, a web tool for teaching print identification, and will be used on the www.graphicsatlas.org website, along with textual information on identification, technology and history information about these reproduction processes.

In-situ X-ray diffraction studies during growth of Ni-Ti shape memory alloy films and their complementary ex-situ characterization

Shape Memory Alloy (SMA) Ni-Ti films have attracted much interest as functional and smart materials due to their unique properties. However, there are still important issues unresolved like formation of film texture and its control as well as substrate effects. Thus, the main challenge is not only the control of the microstructure, including stoichiometry and precipitates, but also the identification and control of the preferential orientation since it is a crucial factor in determining the shape memory behaviour. The aim of this PhD thesis is to study the optimisation of the deposition conditions of films of Ni-Ti in order to obtain the material fully crystallized at the end of the deposition, and to establish a clear relationship between the substrates and texture development. In order to achieve this objective, a two-magnetron sputter deposition chamber has been used allowing to heat and to apply a bias voltage to the substrate. It can be mounted into the six-circle diffractometer of the Rossendorf Beamline (ROBL) at the European Synchrotron Radiation Facility (ESRF), Grenoble, France, enabling an in-situ characterization by X-ray diffraction(XRD) of the films during their growth and annealing. The in-situ studies enable us to identify the different steps of the structural evolution during deposition with a set of parameters as well as to evaluate the effect of changing parameters on the structural characteristics of the deposited film. Besides the in-situ studies, other complementary ex-situ characterization techniques such as XRD at a laboratory source, Rutherford backscattering spectroscopy(RBS), Auger electron spectroscopy (AES), cross-sectional transmission electron microscopy (X-TEM), scanning electron microscopy (SEM), and electrical resistivity (ER) measurements during temperature cycling have been used for a fine structural characterization. In this study, mainly naturally and thermally oxidized Si(100) substrates, TiN buffer layers with different thicknesses (i.e. the TiN topmost layer crystallographic orientation is thickness dependent) and MgO(100) single crystals were used as substrates. The chosen experimental procedure led to a controlled composition and preferential orientation of the films. The type of substrate plays an important role for the texture of the sputtered Ni-Ti films and according to the ER results, the distinct crystallographic orientations of the Ni-Ti films influence their phase transformation characteristics.

Component-based software engineering: a quantitative approach

Dissertação apresentada para a obtenção do Grau de Doutor em Informática pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Characterization of cleaners accidents in the Portuguese service sector

This paper characterizes work accidents at Portuguese industrial cleaning companies, operating in the service sector, through the application of ESAW methodology. Data was codified based on the analysis of 748 accident claims to insurance companies (number of days lost 1 working day) in 3 large industrial cleaning companies for the period 2001-2003. Slipping and falling in the same level was the main deviation from the normal working process in the moment of the accident (in 25% of the accidents); uncoordinated movements was the second cause of accidents (14%); falls of persons to a lower level was the third cause of accidents (~10%), including falls from stairs (~7%) and falls from ladders and mobile ladders (~2%); globally, body movement under or with physical stress, including lifting, carrying, putting down, bending down, twisting, turning, trading badly, twisting leg or ankle and slipping without falling, were the cause in 17% of the accidents. Lower limbs were injured in ~25% of the accidents, hand and fingers in ~14%, the eye in ~4% and the back in ~9% of the accidents. An incidence rate of 3,580 accidents/100,000 employees was found to the sector (2003 data).

Characterization of the volatile fraction emitted by phloems of four pinus species by solid-phase microextraction and gas chromatography–mass spectrometry

Pine forests constitute some of the most important renewable resources supplying timber, paper and chemical industries, among other functions. Characterization of the volatiles emitted by different Pinus species has proven to be an important tool to decode the process of host tree selection by herbivore insects, some of which cause serious economic damage to pines. Variations in the relative composition of the bouquet of semiochemicals are responsible for the outcome of different biological processes, such as mate finding, egg-laying site recognition and host selection. The volatiles present in phloem samples of four pine species, P. halepensis, P. sylvestris, P. pinaster and P. pinea, were identified and characterized with the aim of finding possible host-plant attractants for native pests, such as the bark beetle Tomicus piniperda. The volatile compounds emitted by phloem samples of pines were extracted by headspace solid-phase micro extraction, using a 2 cm 50/30 mm divinylbenzene/carboxen/polydimethylsiloxane table flex solid-phase microextraction fiber and its contents analyzed by high-resolution gas chromatography, using flame ionization and a non polar and chiral column phases. The components of the volatile fraction emitted by the phloem samples were identified by mass spectrometry using time-of-flight and quadrupole mass analyzers. The estimated relative composition was used to perform a discriminant analysis among pine species, by means of cluster and principal component analysis. It can be concluded that it is possible to discriminate pine species based on the monoterpenes emissions of phloem samples.

MBR activated sludge filterability characterization in cross flow filtration

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia do Ambiente, perfil Sanitária

The contribution of multitemporal information from multispectral satellite images for automatic land cover classification at the national scale

Thesis submitted to the Instituto Superior de Estatística e Gestão de Informação da Universidade Nova de Lisboa in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Information Management – Geographic Information Systems

Spectroscopic Studies and Characterization of a Novel Electron-Transfer Chain

A novel two-component enzyme system from Escherichia coli involving a flavorubredoxin (FlRd) and its reductase was studied in terms of spectroscopic, redox, and biochemical properties of its constituents. FlRd contains one FMN and one rubredoxin (Rd) center per monomer. To assess the role of the Rd domain, FlRd and a truncated form lacking the Rd domain (FlRd¢Rd), were characterized. FlRd contains 2.9 ( 0.5 iron atoms/subunit, whereas FlRd¢Rd contains 2.1 ( 0.6 iron atoms/subunit. While for FlRd one iron atom corresponds to the Rd center, the other two irons, also present in FlRd¢Rd, are most probably due to a di-iron site. Redox titrations of FlRd using EPR and visible spectroscopies allowed us to determine that the Rd site has a reduction potential of -140 ( 15 mV, whereas the FMN undergoes reduction via a red-semiquinone, at -140 ( 15 mV (Flox/Flsq) and -180 ( 15 mV (Flsq/Flred), at pH 7.6. The Rd site has the lowest potential ever reported for a Rd center, which may be correlated with specific amino acid substitutions close to both cysteine clusters. The gene adjacent to that encoding FlRd was found to code for an FAD-containing protein, (flavo)rubredoxin reductase (FlRd-reductase), which is capable of mediating electron transfer from NADH to DesulfoVibrio gigas Rd as well as to E. coli FlRd. Furthermore, electron donation was found to proceed through the Rd domain of FlRd as the Rd-truncated protein does not react with FlRd-reductase. In vitro, this pathway links NADH oxidation with dioxygen reduction. The possible function of this chain is discussed considering the presence of FlRd homologues in all known genomes of anaerobes and facultative aerobes.

Fucosyltransferase IX: characterization and biological role

α3/4-Fucosyltransferases (α3/4-FUTs) are glycosyltransferases (GTs) that catalyze the transfer of fucose in an α3/4-linkage onto the N-acetylglucosamine residue from acceptors containing the type II or type I (Galβ4/3GlcNAc, respectively) structures, thus synthesizing the fucosylated Lewis (Le) carbohydrate determinants. Fucosyltransferase IX (FUT9), the most recently identified member of the family, presents the higher divergence from the other FUTs and its sequence is the only highly conserved among species. FUT9 synthesizes the Lewisx (Lex) epitope (Galβ4(Fucα3)GlcNAc). Recent evidence has suggested that it is the enzyme responsible for the synthesis of Lex in the mouse brain. Lex expression has been described in glycoproteins, proteoglycans and glycolipids from the central nervous system (CNS) of diverse species, including rodents and humans.