The presence of CD56/CD16 in T-cell acute lymphoblastic leukaemia correlates with the expression of cytotoxic molecules and is associated with worse response to treatment

Some cases of T-cell acute lymphoblastic leukaemia (ALL) express markers found in natural-killer (NK) cells, such as CD56 and CD16. Out of 84 T-cell ALL cases diagnosed at our Institution, CD56 and/or CD16 was detected in 24 (28.5%), which we designated T/NK-ALL group. Clinical features, laboratory characteristics, survival and expression of cytotoxic molecules were compared in T/NK-ALL and T-ALL patients. Significant differences were observed regarding age (24.9 vs. 16.4 years in T/NK-ALL and T-ALL, respectively, P = 0.006) and platelet counts (177 x 10(9)/l vs. 75 x 10(9)/l in T/NK-ALL and T-ALL, respectively, P = 0.03). Immunophenotypic analysis demonstrated that CD34, CD45RA and CD33 were more expressed in T/NK-ALL patients, whereas CD8 and terminal deoxynucleotidyl transferase were more expressed in T-ALL patients (P < 0.05). The mean overall survival (863 vs. 1869 d, P = 0.02) and disease-free survival (855 vs. 2095 d, P = 0.002) were shorter in patients expressing CD56/CD16. However, multivariate analysis identified CD56/CD16 as an independent prognostic factor only for DFS. Cytotoxic molecules were highly expressed in T/NK-ALL compared to T-ALL. Perforin, granzyme B and TIA-1 were detected in 12/17, 4/17 and 7/24 T/NK-ALL patients and in 1/20, 0/20 and 1/20 T-ALL respectively (P < 0.001, P = 0.036 and P = 0.054). Therefore, the presence of CD56/CD16 was associated with distinct clinical features and expression of cytotoxic molecules in the blasts.

Costimulatory molecules in human periodontal disease tissue

An immunoperoxidase technique was used to examine CD28, CD152, CD80 and CD86 positive cells in gingival biopsies from 21 healthy/gingivitis and 26 periodontitis subjects. The samples were placed into 3 groups (small, intermediate, large) according to the size of the infiltrate. The percent CD28+ T cells in the connective tissue infiltrates was highly variable with no differences between the healthy/gingivitis and periodontitis groups. While there was an increase in positive cells in intermediate infiltrates from both healthy/gingivitis (28.5%) and periodontitis (21.4%) patients compared with small infiltrates (8.6% and 11.8%, respectively), this was not significant, although the percent CD28+ T cells did increase significantly in tissues with increased proportions of B cells relative to T cells (p=0.047). A mean of less than 5% infiltrating T cells were CD152+ which was significantly lower than the mean percent CD28+ T cells in intermediate healthy/gingivitis lesions (p=0.021). The mean percent CD80+ and CD86+ B cells and macrophages was 1–7% and 8–16%, respectively, the difference being significant in intermediate healthy/gingivitis tissues (p=0.012). Analysis of these cells in relation to increasing numbers of B cells in proportion to T cells and also to macrophages, suggested that CD80 was expressed predominantly by macrophages while CD86 was expressed by both macrophages and B cells. Few endothelial cells expressed CD80 or CD86. Keratinocytes displayed cytoplasmic staining of CD80 rather than CD86 although the numbers of positive specimens in the healthy/gingivitis and periodontitis groups reduced with increasing inflammation. In conclusion, percentages of CD28, CD152, CD80 and CD86 did not reflect differences in clinical status. However, the percent CD28+ T cells increased with increasing size of infiltrate and with increasing proportions of B cells suggesting increased T/B cell interactions with increasing inflammation. The percent CD152+ cells remained low indicating that CD152 may not be involved in negative regulation of T cells in periodontal disease. CD80 and CD86 have been reported to promote Th1 and Th2 responses, respectively, and the higher percent CD86+ cells suggests a predominance of Th2 responses in both healthy/gingivitis and periodontitis tissues. Nevertheless, other factors including cytokines themselves and chemokines which modulate T cell cytokine profiles must be monitored to determine the nature of Th1/Th2 responses in periodontal disease.

Identical digeneans in coral reef fishes from French Polynesia and the Great Barrier Reef (Australia) demonstrated by morphology and molecules

Three coral reef fish species, Zanclus cornutus, Chaetodon vagabundus and Naso lituratus, were collected in French Polynesia and on the Great Barrier Reef, Queensland. These fish species were each infected by one morphologically similar digenean species in both localities; Schistorchis Zancli Hanson, 1953 was found in Zanclus cornutus. Preptetos laguncula Bray and Cribb, 1996 in Naso lituratus and Neohypocreadium dorsoporum Machida and Uchida, 1987 in Chaetodon vagabundus. In addition, on the Great Barrier Reef P. laguncula was also found in Naso unicornis and N. dorsoporum in Chaetodon ephippium and Chaetodon flavirostris. Morphometric differences between the species from the two sites were only slight. Sequences from the second internal transcribed spacer of the ribosomal DNA of each worm revealed total homology or negligible divergence between samples from hosts caught in French Polynesia and on the Great Barrier Reef. These results show that across more than 6000 km these digeneans are similar in morphology and genotype. Some species of fishes and molluscs a-re considered to have distributions that encompass the entire tropical Indo-West Pacific. These findings suggest that at least some of their parasites have similarly broad distributions. (C) 2001 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Surface diffusion of adsorbed molecules in porous media: Monolayer, multilayer, and capillary condensation regimes

This review provides an overview of surface diffusion and capillary condensate flow in porous media. Emphasis has been placed on the distinction between purely surface diffusion, multilayer surface diffusion, and, capillary condensate flow.

Erythroid differentiation and protoporphyrin IX down-regulate frataxin expression in Friend cells: characterization of frataxin expression compared to molecules involved in iron metabolism and hemoglobinization

Friedreich ataxia (FA) Is caused by decreased frataxin expression that results in mitochondrial iron (Fe) overload. However, the role of frataxin in mammalian Fe metabolism remains unclear. In this investigation we examined the function of frataxin in Fe metabolism by implementing a well-characterized model of erythroid differentiation, namely, Friend cells induced using dimethyl sulfoxide (DMSO). We have characterized the changes in frataxin expression compared to molecules that play key roles in Fe metabolism (the transferrin receptor [TfR] and the Fe transporter Nramp2) and hemoglobinization (beta-globin). DMSO induction of hemoglobinization results in a marked decrease in frataxin gene (Frda) expression and protein levels. To a lesser extent, Nramp2 messenger RNA (mRNA) levels were also decreased on erythroid differentiation, whereas TfR and beta-globin mRNA levels increased. Intracellular Fe depletion using desferrioxamine or pyridoxal isonicotinoyl hydrazone, which chelate cytoplasmic or cytoplasmic and mitochondrial Fe pools, respectively, have no effect on frataxin expression. Furthermore, cytoplasmic or mitochondrial Fe loading of induced Friend cells with ferric ammonium citrate, or the heme synthesis inhibitor, succinylacetone, respectively, also had no effect on frataxin expression. Although frataxin has been suggested by others to be a mitochondrial ferritin, the lack of effect of intracellular Fe levels on frataxin expression is not consistent with an Fe storage role. Significantly, protoporphyrin IX down-regulates frataxin protein levels, suggesting a regulatory role of frataxin in Fe or heme metabolism. Because decreased frataxin expression leads to mitochondrial Fe loading in FA, our data suggest that reduced frataxin expression during erythroid differentiation results in mitochondrial Fe sequestration for heme biosynthesis. (C) 2002 by The American Society of Hematology.

Non-coding RNAs: multi-tasking molecules in the cell

In the last years it has become increasingly clear that the mammalian transcriptome is highly complex and includes a large number of small non-coding RNAs (sncRNAs) and long noncoding RNAs (lncRNAs). Here we review the biogenesis pathways of the three classes of sncRNAs, namely short interfering RNAs (siRNAs), microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). These ncRNAs have been extensively studied and are involved in pathways leading to specific gene silencing and the protection of genomes against virus and transposons, for example. Also, lncRNAs have emerged as pivotal molecules for the transcriptional and post-transcriptional regulation of gene expression which is supported by their tissue-specific expression patterns, subcellular distribution, and developmental regulation. Therefore, we also focus our attention on their role in differentiation and development. SncRNAs and lncRNAs play critical roles in defining DNA methylation patterns, as well as chromatin remodeling thus having a substantial effect in epigenetics. The identification of some overlaps in their biogenesis pathways and functional roles raises the hypothesis that these molecules play concerted functions in vivo, creating complex regulatory networks where cooperation with regulatory proteins is necessary. We also highlighted the implications of biogenesis and gene expression deregulation of sncRNAs and lncRNAs in human diseases like cancer.

Employment of the side product of biodiesel production in the formation of surfactant like molecules

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Química e Bioquímica

Using gold nanoparticles in protein crystallography: studies in crystal growth and derivatization

Dissertation for the Master Degree in Structural and Functional Biochemistry

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Reactive electron scattering from biomolecules and technologically relevant molecules

The role of a set of gases relevant within the context of biomolecules and technologically relevant molecules under the interaction of low-energy electrons was studied in an effort to contribute to the understanding of the underlying processes yielding negative ion formation. The results are relevant within the context of damage to living material exposed to energetic radiation, to the role of dopants in the ion-molecule chemistry processes, to Electron Beam Induced Deposition (EBID) and Ion Beam Induced Deposition (IBID) techniques. The research described in this thesis addresses dissociative electron attachment (DEA) and electron transfer studies involving experimental setups from the University of Innsbruck, Austria and Universidade Nova de Lisboa, Portugal, respectively. This thesis presents DEA studies, obtained by a double focusing mass spectrometer, of dimethyl disulphide (C2H6S2), two isomers, enflurane and isoflurane (C3F5Cl5) and two chlorinated ethanes, pentachloroethane (C2HCl5) and hexachloroethane (C2Cl6), along with quantum chemical calculations providing information on the molecular orbitals as well as thermochemical thresholds of anion formation for enflurane, isoflurane, pentachloroethane and hexachloroethane. The experiments represent the most accurate DEA studies to these molecules, with significant differences from previous work reported in the literature. As far as electron transfer studies are concerned, negative ion formation in collisions of neutral potassium atoms with N1 and N3 methylated pyrimidine molecules were obtained by time-of-flight mass spectrometry (TOF). The results obtained allowed to propose concerted mechanisms for site and bond selective excision of bonds.

Exploring chemical conversions in metabolic networks by tracing atoms transitions

Dissertação de mestrado em Bioinformática

The contribution of phenolic acids to the anti-inflammatory activity of mushrooms: Screening in phenolic extracts, individual parent molecules and synthesized glucuronated and methylated derivatives

In the present study, the ethanolic extracts of fourteen edible mushrooms were investigated for their anti-inflammatory potential in LPS (lipopolysaccharide) activated RAW 264.7 macrophages. Furthermore the extracts were chemically characterized in terms of phenolic acids and related compounds. The identified molecules (p-hydroxybenzoic, p-coumaric and cinnamic acids) and their glucuronated and methylated derivatives obtained by chemical synthesis were also evaluated for the same bioactivity, in order to establish structure-activity relationships and to comprehend the effects of in vivo metabolism reactions in the activity of the compounds. The extracts of Pleurotus ostreatus, Macrolepiota procera, Boletus impolitus and Agaricus bisporus revealed the strongest anti-inflammatory potential (EC50 values 96 ± 1 to 190 ± 6 µg/mL, and also the highest concentration of cinnamic acid (656 to 156 µg/g), which was also the individual compound with the highest anti-inflammatory activity. The derivatives of p-coumaric acid revealed the strongest properties, specially the derivative methylated in the carboxylic group (CoA-M1) that exhibited similar activity to the one showed by dexamethaxone used as anti-inflammatory standard; by contrast, the derivatives of p-hydroxybenzoic revealed the lowest inhibition of NO production. All in all, whereas the conjugation reactions change the chemical structure of phenolic acids and may increase or decrease their activity, the glucuronated and methylated derivatives of the studied compounds are still displaying anti-inflammatory activity.

Terapéutica farmacológica y de pequeñas moléculas en patologías de atesoramiento lisosomal: focalización en las Lipofuscinosis Ceroideas Neuronales. Farmaceutical and small molecules therapy in lysosomal storage diseases: focus on the Neuronal Ceroid Lipofuscinoses.

Introducción: Las Lipofuscinosis Ceroideas Neuronales (LCNs) son un grupo de patologías neurodegenerativas hereditarias de atesoramiento lisosomal (PALs) caracterizadas por el almacenamiento en los lisosomas de materiales complejos pobremente reconocidos. Su curso es muy severo con desenlace fatal, habiendo sido definidos diversos tipos sobre la base del estudio de los fenotipos clínicos, enzimáticos, morfológicos y las mutaciones. Su incidencia es de 1:12.500 nacimientos vivos a nivel mundial. Las intervenciones farmacológicas con moléculas pequeñas han sido exitosas para algunas PALs; sin embargo, debido a que para cada una de las moléculas ha sido asumido un mecanismo de acción, la efectividad puede estar limitada a uno o a pocos desórdenes y no beneficiar a otros. Se han comprobado efectos diversos de una serie de moléculas tales como Miglustat, Chaperonas moleculares diseñadas, Clenbuterol, N-acetilcisteina (Mucomyst), Cisteamina, Gentamicina y PTC124. Los tratamientos farmacológicos/ con moléculas pequeñas podrían resultar exitosos para las LCNs, mereciendo consideración desarrollar terapias para estos desórdenesObjetivo generalo Investigar en un tipo de patologías del sistema nervioso central, las Lipofuscinosis Ceroideas Neuronales, el enfoque terapéutico-farmacológico con pequeñas moléculas aplicado a otras patologías hereditarias.Objetivos específicoso Desarrollar un prototipo de cultivo de fibroblastos de pacientes a nivel hospitalario en Córdoba y mantener cultivos de fibroblastos de pacientes afectados de una LCN de genotipo CLN2, con mutaciones conocidas. o Enriquecer los cultivos con fármacos/ moléculas pequeñas probadas en otras PALs.o Averiguar si se produce incremento de actividad enzimática de la Tripeptidil Peptidasa-I (TPP-I) lisosomal.Materiales y Métodos: cultivo de fibroblastos de pacientes con el agregado de fármacos/pequeñas moléculas. Los donantes serán diagnosticados en CEMECO a través de una estrategia sistematizada para el reconocimiento de las LCNs y se identificarán las mutaciones en el gen CLN2 causales de enfermedad. Se averiguará la actividad enzimática de TPP-I y se marcará la enzima con anticuerpos específicos en corridas electroforéticas por western blot. Resultados esperados: incrementos en la actividad enzimática de TPP-I en los cultivos celulares con agregado de fármacos/ pequeñas moléculas con respecto a los controles. Importancia del proyecto: se trata de una investigación traduccional (traslational research) en la cual la clínica y los servicios a pacientes se vinculan con la investigación científica, desde una perspectiva de integración. Se desarrolla en un Hospital Público, el Hospital de Niños de la Provincia de Córdoba, asiento del Centro de Estudio de las Metabolopatías Congénitas-CEMECO. Se beneficiarán los pacientes, dado que impactará sobre la calidad de los servicios hospitalarios al suministrar diagnósticos bajo los estándares internacionales, en estrecha vinculación con centros referenciales del exterior. Se obtendrán para los genes de las LCNs los datos del espectro de mutaciones y polimorfismos presentes en la región y se aportarán datos sobre posibilidades de las terapias farmacológicas en relación a cada una de las mutaciones.

Caracterización de moléculas de rizobacterias y de leguminosas con alto impacto productivo y tecnológico en la provincia de Córdoba. Characterization of rhizobacteria and legumes molecules with high production and technological impact in the province of Córdoba.

La provincia de Córdoba cuenta con alto desarrollo agrícola a base de cereales y leguminosas, como por ejemplo el maní. Pero este cultivo con los años ha trasladado su zona de siembra original y se ha extendido hacia otras áreas de mayor riesgo ambiental a raíz de la implantación de la soja. Diversas son las consecuencias de estas dos acciones y que se extienden desde lo agroecológico hasta lo científico-técnico. Este previo estado del arte y las referencias bibliográficas que apuntan a la necesitad de aumentar el valor agregado de los cultivos, nos ha llevado a formular una hipótesis de trabajo y es que las plantas de maní y soja así como las rizobacterias que se asocian con ellas, son productoras de diversas moléculas con potencial uso biológico en la productividad del cultivo y en aplicaciones tecnológicas, biológicas e industriales. Sumado a lo anterior y a las ideas gubernamentales de la necesidad de obtener conocimiento y capitalizarlo como riqueza, y la imperiosa urgencia de responder a demandas regionales, se presenta este proyecto cuyo objetivo general apunta a estudiar la producción de diversas moléculas de rizobacterias y leguminosas con el fin de mejorar la productividad de los cultivos y desarrollar nuevas aplicaciones tecnológicas en la provincia de Córdoba. Para cumplir dentro de los dos años de trabajo solicitados con lo expuesto anteriormente, la investigación será dividida en objetivos específicos y que consisten en investigar la producción de moléculas de raíces de maní y soja, analizar la respuesta microbiana a las rizodeposiciones de ambas leguminosas y evaluar el posible papel biológico y aplicación tecnológica de moléculas de ambos tipos de organismos. Nuestro grupo es de caracter multidisciplinar y ahondará en la diversidad molecular producida por raíces de maní y soja en direfentes días y la respuesta de las rizobacterias que se asocian ellas utilizando técnicas químicas (HPLC, GC, GC-masa) y herramientas microbiológicas y bioquímicas clásicas. Con fines de aplicación tecnológica se determinará la posible acción antioxidante de los extractos vegetales sobre sistemas modelos de ensayo así como la búsqueda de enzimas y hormonas microbianas aplicables en otros campos de la ciencia. De esta forma se pretende atender algunas demandas de diferentes sectores del centro sur de Córdoba y del país pero fundamentalmente posibilitar nuevas aplicaciones de las leguminosas y de las rizobacterias además de permitir la formación académicas de alumnos de grado y posgrado de la UNRC. The province of Cordoba has high agricultural development based on cereals and legumes such as peanuts. But the crop over the years has transferred his original planting area and has spread to other areas of greatest environmental risk following the introduction of soybeans. The previous state and regional art references that point to the necessity of increasing the value-added crops, has led us to formulate a working hypothesis is that the peanut and soybean plants and rhizobacteria associated with they are products of various biological molecules with potential use in crop productivity and biological technology and industrial applications. The general objective is aimed at studying the production of various molecules and legumes rhizobacteria to improve crop productivity and develop new technological applications in the Cordoba province. This form is intended to meet some demands of different sectors of the center south of Cordoba and the country but enabling new applications of legumes and rhizobacteria in addition to allowing the academic training of undergraduates and graduate of the UNRC.

Aspects of immunity for the AMA-1 family of molecules in humans and non-human primates malarias

The apical membrane antigen (AMA-1) family of malaria merozoite proteins is characterised by a high degree of inter-species conservation. Evidence that the protein (PK66/AMA-1) from the simian parasite Plasmodium knowlesi was protective in rhesus monkeys suggested that the 83kDa P. falciparum equivalent (PF83/AMA-1) should be investigated for protective effects in humans. Here we briefly review pertinent comparative data, and describe the use of an eukaryotic full length recombinant PF83/AMA-1 molecule to develop a sensitive ELISA for the determination of serological responses in endemic populations. The assay has revealed surprisingly high levels of humoral response to this quantitatively minor antigen. We also show that PK66/AMA-1 inhibitory mAb's are active against merozoites subsequent to release from schizont-infected red cells, further implicating AMA-1 molecules in red cell invasion.