Evaluation of inflammatory response induced by different types of daily contact lenses

Dissertação de mestrado em Genética Molecular

The role of macroH2A1 in prostate carcinogenesis

Dissertação de mestrado em Genética Molecular

Metabolismo de las Purinas y Pirimidinas: Errores hereditarios primarios y alteraciones secundarias en otros defectos genéticos

En este trabajo se propuso el estudio de los desórdenes genéticos en el metabolismo de las purinas (Pu) y pirimidinas (Pi), debido a que dentro del amplio espectro de enfermedades metabólicas hereditarias (EMH) que fueron identificándose en nuestro medio no se incluían estas entidades, probablemente por el desconocimiento de su existencia y también por la carencia de la metodología necesaria para su pesquisa. Hasta el presente fueron identificados veintitrés defectos hereditarios que involucran las enzimas esenciales del metabolismo de las Pu y Pi, diecisiete de ellos asociados con serias consecuencias clínicas; los sistemas frecuentemente afectados son: inmunológico, hematológico, neurológico y renal. Defectos enzimáticos en este metabolismo, como por ejemplo el de la enzima Tiopurina S-metiltransferasa (TPMT), pueden provocar también intolerancia al tratamiento de diversas enfermedades con drogas análogas a las Pu y Pi. Los principios de identificación de los desórdenes de las Pu y Pi comprenden la investigación del producto del gen anormal, es decir esencialmente la aplicación de la genética bioquímica que estudia: a) el defecto genético evaluando la consecuencia del bloqueo de la vía metabólica normal por deficiencia de los productos o por acumulación de los precursores de estos metabolitos; b) la actividad enzimática específica, la cual puede presentar una deficiencia total, parcial o sobreactividad. Además se puede aplicar la genética molecular, es decir la investigación de las mutaciones responsables del defecto metabólico de utilidad para la confirmación diagnóstica y para establecer correlaciones genotipo-fenotipo. El estudio abarcó tres áreas estrictamente relacionadas con el tópico central, el metabolismo de las Pu y Pi, y concatenadas en sus objetivos específicos: I. Investigación de las enfermedades genéticas de las Pu y Pi. Objetivo: - Reconocer las EMH-PuPi a través de un protocolo selectivo que permita definir las alteraciones bioquímicas, enzimáticas y moleculares en pacientes presuntos de padecer estos defectos. II. Investigación del polimorfismo genético de la TPMT en la población argentina. Objetivo: - Investigar el polimorfismo genético de la TPMT, fenotipo bioquímico (actividad enzimática) - genotipo (mutaciones), en la población argentina debido a que esta enzima es un excelente ejemplo del potencial impacto de la farmacogenética en medicina. II. Investigación de posibles mecanismos de excitotoxicidad y deficiencia energética en pacientes con diferentes EMH mediante el análisis de bases y nucleósidos en el LCR. Objetivo: - Establecer posibles interacciones entre otras vías comprometidas con la del metabolismo de las Pu y Pi en EMH de exacta nosología.

Evolución de las poblaciones humanas originarias en la región central de Argentina: Nuevas evidencias bioantropológicas y arqueológicas. Evolution of the native human populations in the central territory of Argentina: New bioanthropological and archaeological evidences.

El presente proyecto retoma los interrogantes acerca de los movimientos de población humana que se sucedieron en el area central de Argentina (actual territorio de Córdoba y parte de San Luis), desde los primeros asentamientos hasta la Conquista, valiéndose de la información proporcionada por la arqueología, la antropología física y la genética molecular, de manera interdisciplinaria. Con base en investigaciones previas realizadas por nuestro grupo y otros autores, se aplicarán nuevas metodologías y enfoques teóricos para echar luz sobre interrogantes acerca de las probables vías de poblamiento de la región y la evolución local de esas poblaciones. Se someterán a prueba hipótesis migratorias y de colonización, incluyendo estos eventos locales en un contexto más general sobre los procesos ocurridos a nivel regional y continental. Para los datos biológicos moleculares y morfológicos se emplearán técnicas de filogeografía (distribución espacial de linajes mitocondriales y del cromosoma Y) y genética del paisaje (autocorrelación espacial, kriging, barreras genéticas). La perspectiva arqueológica del proyecto intenta desde los análisis de diseño y función en instrumentos líticos discutir expectativas en cuanto a la permanencia o no de ciertas formas de diseño a través del tiempo, comparando conjuntos tempranos (asociados a tecnología "Fell 1") con otros de épocas posteriores. Esta línea se llevará a cabo utilizando la comparación entre los materiales provenientes de excavaciones estratigráficas para realizar análisis tecno-morfológicos sensu Aschero (1975-1983) y análisis de microhuellas de uso que nos permiten hablar de la función en los filos líticos. Esta línea se complementa con el desarrollo de programas experimentales de estudio sobre las diversas materias primas líticas utilizadas en el pasado en ambas áreas (Chert, vulcanita, cuarzo y calcedonia, entre las principales). Ambos enfoques nos permitirán evaluar la posible existencia de variaciones tecnológicas locales producto de procesos adaptativos o modos de producción o uso diferenciales. Una segunda línea propone el estudio del paisaje y los recursos líticos en la región utilizando SIG. Con respecto a esta perspectiva de investigación se postula analizar la forma en la cual los cazadores-recolectores utilizaron el espacio desde fines del Pleistoceno/Holoceno Temprano hasta el Holoceno Tardío partiendo de un conocimiento profundo de la distribución de los recursos líticos. En particular, conocer y discutir distintos aspectos de la disponibilidad, tipo, calidad y accesibilidad a las rocas. Este enfoque es fundamental para entender los procesos de elección y uso de estos recursos en el pasado logrando entender las diversas formas de organización de la tecnología.

Estudi de la diversitat de picoflagel·lats heterotròfics a la zona de Blanes mitjançant tècniques moleculars i de cultiu

S’ha estudiat la diversitat de picoflagel—·lats heterotròfics, d’aigües del nord-oest del mar Mediterrani, mitjançant DGGE , biblioteques de clons i enriquiments. S’ha trobat que la diversitat és alta (índex Shannon 2,227), com en d’altres estudis, però que disminueix en afegir matèria orgànica (extracte de llevat o d’arròs), amb índex de Shannon de fins a 0,731. Per una entrada d’aigua continental rica en nutrients, s’han desenvolupat millor les crisofícies en detriment d’altres organismes habituals al medi marí, com els MAST.

Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility

Background: Germline genetic variation is associated with the differential expression of many human genes. The phenotypic effects of this type of variation may be important when considering susceptibility to common genetic diseases. Three regions at 8q24 have recently been identified to independently confer risk of prostate cancer. Variation at 8q24 has also recently been associated with risk of breast and colorectal cancer. However, none of the risk variants map at or relatively close to known genes, with c-MYC mapping a few hundred kilobases distally. Results: This study identifies cis-regulators of germline c-MYC expression in immortalized lymphocytes of HapMap individuals. Quantitative analysis of c-MYC expression in normal prostate tissues suggests an association between overexpression and variants in Region 1 of prostate cancer risk. Somatic c-MYC overexpression correlates with prostate cancer progression and more aggressive tumor forms, which was also a pathological variable associated with Region 1. Expression profiling analysis and modeling of transcriptional regulatory networks predicts a functional association between MYC and the prostate tumor suppressor KLF6. Analysis of MYC/Myc-driven cell transformation and tumorigenesis substantiates a model in which MYC overexpression promotes transformation by down-regulating KLF6. In this model, a feedback loop through E-cadherin down-regulation causes further transactivation of c-MYC.Conclusion: This study proposes that variation at putative 8q24 cis-regulator(s) of transcription can significantly alter germline c-MYC expression levels and, thus, contribute to prostate cancer susceptibility by down-regulating the prostate tumor suppressor KLF6 gene.

Comparative analysis of cancer genes in the human and chimpanzee genomes

Background: Cancer is a major medical problem in modern societies. However, the incidence of this disease in non-human primates is very low. To study whether genetic differences between human and chimpanzee could contribute to their distinct cancer susceptibility, we have examined in the chimpanzee genome the orthologous genes of a set of 333 human cancer genes. Results: This analysis has revealed that all examined human cancer genes are present in chimpanzee, contain intact open reading frames and show a high degree of conservation between both species. However, detailed analysis of this set of genes has shown some differences in genes of special relevance for human cancer. Thus, the chimpanzee gene encoding p53 contains a Pro residue at codon 72, while this codon is polymorphic in humans and can code for Arg or Pro, generating isoforms with different ability to induce apoptosis or interact with p73. Moreover, sequencing of the BRCA1 gene has shown an 8 Kb deletion in the chimpanzee sequence that prematurely truncates the co-regulated NBR2 gene. Conclusion: These data suggest that small differences in cancer genes, as those found in tumor suppressor genes, might influence the differences in cancer susceptibility between human and chimpanzee. Nevertheless, further analysis will be required to determine the exact contribution of the genetic changes identified in this study to the different cancer incidence in non-human primates.

Structural and functional properties of genes involved in human cancer

Background: One of the main goals of cancer genetics is to identify the causative elements at the molecular level leading to cancer.Results: We have conducted an analysis of a set of genes known to be involved in cancer in order to unveil their unique features that can assist towards the identification of new candidate cancer genes. Conclusion: We have detected key patterns in this group of genes in terms of the molecular function or the biological process in which they are involved as well as sequence properties. Based on these features we have developed an accurate Bayesian classification model with which human genes have been scored for their likelihood of involvement in cancer.

Array-CGH in patients with a clinical diagnosis of Kabuki syndrome: identification of two cases with terminal 2q37 deletion and no other recurrent rearrangement

Background: Kabuki syndrome (KS) is a multiple congenital anomaly syndrome characterized by specific facial features, mild to moderate mental retardation, postnatal growth delay, skeletal abnormalities, and unusual dermatoglyphic patterns with prominent fingertip pads. A 3.5 Mb duplication at 8p23.1-p22 was once reported as a specific alteration in KS but has not been confirmed in other patients. The molecular basis of KS remains unknown. Methods: We have studied 16 Spanish patients with a clinical diagnosis of KS or KS-like to search for genomic imbalances using genome-wide array technologies. All putative rearrangements were confirmed by FISH, microsatellite markers and/or MLPA assays, which also determined whether the imbalance was de novo or inherited. Results: No duplication at 8p23.1-p22 was observed in our patients. We detected complex rearrangements involving 2q in two patients with Kabuki-like features: 1) a de novo inverted duplication of 11 Mb with a 4.5 Mb terminal deletion, and 2) a de novo 7.2 Mb-terminal deletion in a patient with an additional de novo 0.5 Mb interstitial deletion in 16p. Additional copy number variations (CNV), either inherited or reported in normal controls, were identified and interpreted as polymorphic variants. No specific CNV was significantly increased in the KS group. Conclusion: Our results further confirmed that genomic duplications of 8p23 region are not a common cause of KS and failed to detect other recurrent rearrangement causing this disorder. The detection of two patients with 2q37 deletions suggests that there is a phenotypic overlap between the two conditions, and screening this region in the Kabuki-like patients should be considered.

Hereditary hepatic and systemic amyloidosis caused by a new deletion/insertion mutation in the apolipoprotein AI gene.

We report a Spanish family with autosomal-dominant non-neuropathic hereditary amyloidosis with a unique hepatic presentation and death from liver failure, usually by the sixth decade. The disease is caused by a previously unreported deletion/insertion mutation in exon 4 of the apolipoprotein AI (apoAI) gene encoding loss of residues 60-71 of normal mature apoAI and insertion at that position of two new residues, ValThr. Affected individuals are heterozygous for this mutation and have both normal apoAI and variant molecules bearing one extra positive charge, as predicted from the DNA sequence. The amyloid fibrils are composed exclusively of NH2-terminal fragments of the variant, ending mainly at positions corresponding to residues 83 and 92 in the mature wild-type sequence. Amyloid fibrils derived from the other three known amyloidogenic apoAI variants are also composed of similar NH2-terminal fragments. All known amyloidogenic apoAI variants carry one extra positive charge in this region, suggesting that it may be responsible for their enhanced amyloidogenicity. In addition to causing a new phenotype, this is the first deletion mutation to be described in association with hereditary amyloidosis and it significantly extends the value of the apoAI model for investigation of molecular mechanisms of amyloid fibrillogenesis.

Precursor uptake assays and metabolic analyses in isolated tomato fruit chromoplasts

Background Carotenoids are the most widespread group of pigments found in nature. In addition to their role in the physiology of the plant, carotenoids also have nutritional relevance as their incorporation in the human diet provides health benefits. In non-photosynthetic tissues, carotenoids are synthesized and stored in specialized plastids called chromoplasts. At present very little is known about the origin of the metabolic precursors and cofactors required to sustain the high rate of carotenoid biosynthesis in these plastids. Recent proteomic data have revealed a number of biochemical and metabolic processes potentially operating in fruit chromoplasts. However, considering that chloroplast to chromoplast differentiation is a very rapid process during fruit ripening, there is the possibility that some of the proteins identified in the proteomic analysis could represent remnants no longer having a functional role in chromoplasts. Therefore, experimental validation is necessary to prove whether these predicted processes are actually operative in chromoplasts. Results A method has been established for high-yield purification of tomato fruit chromoplasts suitable for metabolic studies. Radiolabeled precursors were efficiently incorporated and further metabolized in isolated chromoplast. Analysis of labeled lipophilic compounds has revealed that lipid biosynthesis is a very efficient process in chromoplasts, while the relatively low incorporation levels found in carotenoids suggest that lipid production may represent a competing pathway for carotenoid biosynthesis. Malate and pyruvate are efficiently converted into acetyl-CoA, in agreement with the active operation of the malic enzyme and the pyruvate dehydrogenase complex in the chromoplast. Our results have also shown that isolated chromoplasts can actively sustain anabolic processes without the exogenous supply of ATP, thus suggesting that these organelles may generate this energetic cofactor in an autonomous way. Conclusions We have set up a method for high yield purification of intact tomato fruit chromoplasts suitable for precursor uptake assays and metabolic analyses. Using targeted radiolabeled precursors we have been able to unravel novel biochemical and metabolic aspects related with carotenoid and lipid biosynthesis in tomato fruit chromoplasts. The reported chromoplast system could represent a valuable platform to address the validation and characterization of functional processes predicted from recent transcriptomic and proteomic data.

Characterization of Arabidopsis FPS isozymes and FPS gene expression analysis provide insight into the biosynthesis of isoprenoid precursors in seeds

Arabidopsis thaliana contains two genes encoding farnesyl diphosphate (FPP) synthase (FPS), the prenyl diphoshate synthase that catalyzes the synthesis of FPP from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In this study, we provide evidence that the two Arabidopsis short FPS isozymes FPS1S and FPS2 localize to the cytosol. Both enzymes were expressed in E. coli, purified and biochemically characterized. Despite FPS1S and FPS2 share more than 90% amino acid sequence identity, FPS2 was found to be more efficient as a catalyst, more sensitive to the inhibitory effect of NaCl, and more resistant to thermal inactivation than FPS1S. Homology modelling for FPS1S and FPS2 and analysis of the amino acid differences between the two enzymes revealed an increase in surface polarity and a greater capacity to form surface salt bridges of FPS2 compared to FPS1S. These factors most likely account for the enhanced thermostability of FPS2. Expression analysis of FPS::GUS genes in seeds showed that FPS1 and FPS2 display complementary patterns of expression particularly at late stages of seed development, which suggests that Arabidopsis seeds have two spatially segregated sources of FPP. Functional complementation studies of the Arabidopsis fps2 knockout mutant seed phenotypes demonstrated that under normal conditions FPS1S and FPS2 are functionally interchangeable. A putative role for FPS2 in maintaining seed germination capacity under adverse environmental conditions is discussed.

SSCP-polymorphism in intron 12 of the CFTR gene recognized by BclI

Source/Description: SSCP analysis of intron 12 of the CFTR gene from PCR products showed an extra band in several DNA samples. Sequencing of the additional fragment extra band revealed a T- A change in the position 1898 + 152 of CFTR (Fig. 1). The change is a polymorphism which can be identified by SSCP or by BclI digestion...

PCR detection of the pKM.19/ScrfI RFLP (D7S23), a marker closely linked to the cystic fibrosis mutation

Source: Description: pKM-19 is a 1.0 kb EcoRI human genomic fragment inserted in pUC13, that detects a Scrfl (CC/NGG) RFLP (1, 2). We report here the primer sequences suitable for the detection of this RFLP by PCR...

Characterization of alternatively spliced products and tissue-specific isoforms of USP28 and USP25

Background: The ubiquitin-dependent protein degradation pathway is essential for the proteolysis of intracellular proteins and peptides. Deubiquitinating enzymes constitute a complex protein family involved in a multitude of cellular processes. The ubiquitin-specific proteases (UBP) are a group of enzymes whose predicted function is to reverse the ubiquitinating reaction by removing ubiquitin from a large variety of substrates. We have lately reported the characterization of human USP25, a specific-ubiquitin protease gene at 21q11.2, with a specific pattern of expression in murine fetal brains and adult testis. Results: Database homology searches at the DNA and protein levels and cDNA library screenings led to the identification of a new UBP member in the human genome, named USP28, at 11q23. This novel gene showed preferential expression in heart and muscle. Moreover, cDNA, expressed sequence tag and RT-PCR analyses provided evidence for alternatively spliced products and tissue-specific isoforms. Concerning function, USP25 overexpression in Down syndrome fetal brains was shown by real-time PCR. Conclusions: On the basis of the genomic and protein sequence as well as the functional data, USP28 and USP25 establish a new subfamily of deubiquitinating enzymes. Both genes have alternatively spliced exons that could generate protein isoforms with distinct tissue-specific activity. The overexpression of USP25 in Down syndrome fetal brains supports the gene-dosage effects suggested for other UBP members related to aneuploidy syndromes.