ROMERO, José Camilo Torres. Análise proteômica do plasma de pacientes portadores de síndrome mielodisplásica do tipo areb e arsa utilizando lectinas vegetais. 2016. 104 f. Tese (Doutorado em Bioquímica)-Universidade Federal do Ceará, Fortaleza, 2016. / Submitted by Anderson Silva Pereira (anderson.pereiraaa@gmail.com) on 2017-05-03T20:55:53Z No. of bitstreams: 1 2016_tese_jctromero.pdf: 2418639 bytes, checksum: f9af8288a0c70314148c067bb2ed7ae5 (MD5) / Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2017-05-18T23:10:09Z (GMT) No. of bitstreams: 1 2016_tese_jctromero.pdf: 2418639 bytes, checksum: f9af8288a0c70314148c067bb2ed7ae5 (MD5) / Made available in DSpace on 2017-05-18T23:10:09Z (GMT). No. of bitstreams: 1 2016_tese_jctromero.pdf: 2418639 bytes, checksum: f9af8288a0c70314148c067bb2ed7ae5 (MD5) Previous issue date: 2016 / The myelodysplastic syndromes (Myelodysplastic Syndrome MDS) are diseases that occur when blood-producing cells are damaged bone marrow. This causes damage to one or moretypes of blood cells because its production is defective. MDS is considered a type of cancer and often end up being melodie acute leukemia (AML). The most common types of these syndromes are refractory anemia with ringed sideroblasts (ARSA) and anemia refractory with Excess Blasts (AREB). This study aimed to carry out the proteomic analysis of spinal cord serum of pediatric patients with any of the syndromes for the identification of proteins that are potential candidates for biological markers for evaluation, study and diagnosis of disease. The samples from ten patients with ARSA, tem with AREB and Ten healthy persons (control) were compared. These were subjected to immunodepletion, affinity chromatography with lectin galactose-linker selected by the anomeric recognition profile using chromatography in crosslinked hemicelulases, the selected lectins were subsequently immobilized in Sepharose 4B, the serum bone marrow samples were digested for subsequent analysis by mass spectrometry. The softwareExpressionE, based on protein expression levels, calculated the ratio between the selected groups, so 7 proteins have been identified as possible candidates for the biomarker syndromes. The overexpression of Vitronectin (VTN), fibrinogen (FGA), Pregnancy zone protein (PZP), Kininogen (KNG1) Immunoglobulin lambda chain (IGL), complement factor C4b (CB4) and Hemopexin (HPX) compared with the group control, seems to be an indicator of syndromes and were selected to form a panel of potential candidates for prognostic biomarkers. The only recognition by the frutalin to Clusterin (CLU) and Vitronectin in ARSA and Fibrinogen to AREB, do lectin a very useful tool to differentiate syndromes in proteomics studios. / As Síndromes Mielodisplásicas (SMD) são doenças que ocorrem quando as células produtoras de sangue são danificadas na medula óssea e esses danos podem afetar um ou mais tipos de células sanguíneas. Os tipos mais comuns de SMD são a Anemia Refratariacom Sideroblastos em Anel (ARSA) e Anemia Refratariacom Excesso de Blastos (AREB). Este trabalho teve como objetivo realizar a análise proteômica do plasmamedular de pacientes com SMD tipo ARSA e AREB, visando àidentificação de proteínas que sejam potenciais candidatas a marcadores biológicos para avaliação, estudo e diagnóstico dessas doenças. Amostras de plasmade dez pacientes com ARSA, dez com AREB e dez indivíduos saudáveis (Controle) foram selecionadas para análise proteômica. Estas foram submetidas à imunodepleção, cromatografia de afinidade com lectina α-D-galactose-ligante de sementes de Artocarpus incisa imobilizada em SepharoseTM 4B, concentradas e digeridas para posterior análise por espectrometria de massas. O programa ExpressionE, baseado nos níveis de expressão das proteínas, calculou a razão entre os grupos selecionados. Foram identificadas 7 proteínas potenciais candidatas a biomarcadores, tais como a Vitronectina (VTN), Fibrinogênio (FGA), Pregnancy zone protein (PZP), Cininogênio (KNG1), Cadeia de Imunoglobulina Lambda (IGLL1), Factor do complemento Cb4 (Cb4) e Hemopexina (HPX), por estarem super expressas no grupo de pacientes com SMD, em ambos os tipos, ao se comparar com o grupo controle (indivíduos sadios). Estas foram selecionadas para formar um painel de proteínas candidatas biomarcadoresde diagnóstico da SMD. O reconhecimento único por parte da frutalina para Clusterina (CLU) e Vitronectina em ARSA e Fibrinogenio para AREB, torna essa lectina, uma ferramenta muito útil para diferenciar as SMD em estudos proteômicos.

The nitrogenase enzyme is the biochemical machiner responsible for the conversion of the largely unavailable nitrogen to the easily assimilable ammonia for living organisms by the process termed as biological nitrogen fixation (BNF). This study was focused on understanding the various structural and functional aspects of the nitrogenase enzyme related to maturation and assembly of the FeMo-cofactor (FeMoco) metallocluster of the MoFe protein (the site for final substrate reduction), development of a dimeric MoFe protein and the structural homology of nitrogenase with other metalloenzymes. This research was specifically directed towards the NifHDKX proteins in which the nifHDK genes are the major structural genes that encode the nitrogenase enzyme and nifX is an accessory gene that encodes the NifX protein, indicated to be involved in the formation of the FeMoco. The overall objective of this study was to gain structural and functional information on the nitrogenase enzyme through the study of the NifHDKX proteins. A major part of our study included the detection of protein-protein interactions between the NifD, NifK and a fused NifDK protein. The results of this study could prove to be useful for further studies that are directed towards condensing the nif genes so as to facilitate transfer of nitrogen fixing genes to plants for their improved nutrition. We also determined protein-protein interactions between NifX and other proteins involved in the FeMoco biosynthetic pathway. Based on the results, we were able to describe the role of NifX and propose a modified model for the FeMoco biosynthesis pathway. Apart from this, a comparative structural and evolutionary study was performed on the NifH similar proteins such as ChlL, CompA, MinD and ArsA and the NifDK similar proteins known as ChlBN. Based on the conservation of similar structural domains in NifH and ArsA, NifH was found to complement the function of ArsA1. Also the comparison between NifDK and the homology modeled ChlBN protein structure suggested a potential site for the presence of a FeMoco in ChlN. Thus, these studies helped us to derive meaningful conclusions on the structure and evolution of the nitrogenase enzyme and its homologs in nature.

The E. coli ArsA is involved in arsenic detoxification but the role of yArsA (ArsA homologue of Saccharomyces cerevisiae, encoded by YDL100c ORF) in yeast is still undefined. Disruption of YDL100c ORF is not lethal but the disrupted strain (KO) shows decreased thermotolerance. To study the role of yArsA in thermotolerance, wild type (WT) and KO were grown at 25¢Jand 37¢J, and assayed for the intracellular levels of trehalose accumulation and molecular oxidation, and the biosynthesis of heat shock proteins. The results show that molecular oxidation is higher and trehalose accumulation is lower in KO compared with WT grown at 37¢J, suggesting that increased ROS and decreased trehalose content are the cause of cell death. Further analysis of the expression of ROS defense mechanisms show that there is no significant difference in TSL1 and SOD1 expression in WT and KO grown at 25¢J or 37¢J but the CTT1 expression in KO was much less than WT grown at 37¢J. These observations are consistent with the assays of enzymatic activity of catalase and antioxidant GSH contents. Loss of catalase activity, decreased trehalose contents and Hsp104p expression suggest a deficiency in activation of general but not specific stress response in KO when grown at 37¢J. Therefore, yArsA was involved in signaling the general stress response in stress tolerance network.

Chez les ruminants, l’Acidose Ruminale SubAiguë (ARSA) est une maladie d’origine nutritionnelle qui fait suite à une perturbation des fermentations microbiennes et à une acidité anormale du compartiment ruminal. L’installation chronique de ce dysfonctionnement digestif peut avoir une incidence néfaste sur l’efficacité de production et la santé des animaux. À l’échelle de l’individu ou du troupeau, elle aura pour conséquences des retombées économiques négatives pour l’éleveur. Un des problèmes majeurs de cette maladie est qu’elle ne se manifeste pas par des signes cliniques spécifiques. A l’heure actuelle, seul le pH ruminal permet d’objectiver la maladie même si aucun indicateur de pH ne fait l’unanimité, notamment du fait des variabilités importantes liées à la technique de mesure du pH d’une part et à la susceptibilité des animaux d’autre part. Dans ce contexte, cette thèse a eu pour objectif d’améliorer le diagnostic individuel de l’ARSA chez la vache laitière en développant une approche multiparamétrique applicable sur le terrain. Nous proposons de nouveaux indicateurs issus de cinétiques de pH mesuré de façon non-invasive avec des bolus intra-ruminaux. Ces nouveaux indicateurs relatifs, calculés quotidiennement sur les cinétiques normalisées sur 0 (NpH), sont le temps passé sous NpH <-0,3, l’écart type et l’amplitude. Ils permettent de pallier les fortes sources de variabilité et présentent l’intérêt d’être transposables entre études et sont plus précis pour caractériser l’ARSA. Parallèlement, nous avons développé des modèles multiparamétriques composés de plusieurs paramètres mesurés simultanément dans différents compartiments biologiques (lait, fèces, salive, sang, urine) ou sur l’animal (comportement). Leur capacité de prédiction de l’ARSA a ensuite été évaluée en élevage. Certains modèles incluant des paramètres périphériques au rumen et simples à mesurer sur le terrain présentent une bonne sensibilité (concentration en urée dans le lait, en bicarbonate dans le sang, pH salivaire), et d’autres ont une bonne spécificité (nombre de buvées de l’animal, pH fécal, concentration en urée dans le lait). Néanmoins, aucun modèle ne renferme un couple sensibilité et spécificité satisfaisant. A l’issue de ce travail nous proposons une stratégie diagnostique fondée sur 4 étapes : 1) l’analyse du contexte de diagnostic de l’ARSA, 2) l’évaluation des facteurs de risques, 3) l’évaluation des modèles multiparamétriques et 4) le calcul d’indicateurs NpH ruminaux des individus à risque. / In ruminants, subacute ruminal acidosis (SARA) is a nutritional disease that induces an abnormal acidity of the rumen compartment as well as disturbance in microbial fermentation. When the disease becomes chronic, it can lead to negative effects on production efficiency and animal health at the individual or the herd scales, with negative economic consequences for the farmer. One of the major problems of SARA is that there are no obvious clinical signs. Presently, the only benchmark to define SARA is rumen pH. However, no pH indicator is unanimous due to the important variability related both to the measurement technique itself and to the animal susceptibility. In this context, this thesis aimed to improve the individual diagnosis of SARA in dairy cows by developing a multiparametric approach that could be used on field. We propose new indicators of pH kinetics measured noninvasively with intra-ruminal boluses. These new relative indicators, calculated daily (kinetic normalised on 0, NpH), consist of the time spent under NpH < - 0.3, the NpH standard deviation and the NpH range. These indicators make it possible to overcome the strong sources of variability and have the advantage of being transposable while being more accurate to characterize SARA. At the same time, we have developed multiparametric models including a number of parameters measured simultaneously in various biological compartments (milk, faeces, saliva, blood, urine) or on animal behaviour. The models ability to predict SARA has been evaluated on field. Some models including rumen peripheral parameters (concentration of urea in milk, of bicarbonate in blood, salivary pH) have a proficient sensitivity while others have a proficient specificity (number of drinking acts, faecal pH, and urea concentration in milk). However, no model developed is both sensitive and specific enough. The diagnostic strategy we propose is based on 4 steps: 1) analysis of the SARA diagnostic context, 2) assessment of risk factors, 3) evaluation of multiparametric models and (4) determination of ruminal NpH indicators for individuals presenting a high risk of SARA.

Metachromatic leukodystrophy (MLD) and Gaucher disease (GD) are caused by a deficiency of arylsulphatase A (ASA) and b-glucocerebrosidase (GBA), respectively. They are lysosomal storage disorders with a heterogeneous clinical spectrum encompassing visceral, skeletal and neurologic involvement resulting in high morbidity and mortality. The overall aim of this study is to elucidate the genetic component/s of high ASA and GBA enzyme activity in normal healthy individuals with the ultimate goal of using this information to produce greater protein activity from a recombinant protein. A wide variation in ASA and GBA enzyme activity levels has been observed in the normal population. The first objective of this project was to identify and characterise single nucleotide polymorphisms (SNPs) in the arylsulphatase A (ARSA) and glucocerebrosidase (GBA) genes that are responsible for determining the levels of expressed enzyme activity in the normal population. The second objective was to assess the contribution of transcriptional regulation and TCP80 mediated translational control to normal enzyme variation. TCP80, a translational control protein that interacts with the GBA coding region, is a splice variant of the interleukin binding factor 3 (ILF3) gene. Ten samples from individuals with high ASA activity and twenty samples from individuals with high GBA activity were screened for polymorphisms via denaturing high pressure liquid chromatography (dHPLC) and sequencing. The frequency of these polymorphisms in the normal population was determined using dot-blot hybridisation. Fifteen ARSA polymorphisms (4 promoter, 5 coding, 5 intronic and 1 poly(A) signal) and two GBA polymorphisms (1 intronic and 1 in 3¢-UTR) were identified. Two low frequency ASA polymorphisms (2723A > G, W193C) were found to be correlated with low activity, while another low frequency ASA polymorphism (1101+123C > T) was found to be correlated with high activity in a population of 113 individuals. Real time PCR was used to measure mRNA levels of GBA, ASA and LF3 along with enzyme activity levels of GBA and ASA in two cell types (leucocytes and skin fibroblasts) from four healthy individuals and seven cell lines (HL60, THP1, Huh7, U118, SW1353, Hep G2, and B-cells). Transcriptional control was evident for all three genes with GBA mRNA levels varying over 30 fold, ASA mRNA levels varying over seven fold and ILF3 levels varying more than 24 fold. The 5¢-flanking region of GBA was investigated for the cis-elements responsible for tissue-specific expression. However, it was not possible to demonstrate that the cis-element region was influencing GBA expression. Translational efficiency was measured using the magnitude of the mRNA:enzyme activity ratio as an indicator. GBA translational inefficiency was most pronounced in B cells which require four times more mRNA molecules than hepatocytes (Hep G2) and over 25 times more mRNA molecules than chondrocytes (SW1353) to produce one unit of GBA enzyme activity. Except in B-cells, GBA translational efficiency appears to increase as ILF3 mRNA levels decrease. The tissue-specific variation observed in the protein levels of the ILF3 splice variants, TCP80 and DRBP76, may play a role. The correlation of several low frequency SNPs with low ASA enzyme activity or high ASA activity indicates a role in determining the distribution of enzyme activity levels in the normal population. However, there do not appear to be any common high activity polymorphisms. Knowledge of the exact mechanisms responsible for the observed transcriptional and translational control of these lysosomal genes will greatly enhance the understanding of genotype-phenotype correlation and the contribution of genetic variants to natural variation.