Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Análise de fragmentos arqueológicos: um diálogo entre a Química, Biologia e Arqueologia

Dissertação de mestrado em Técnicas de Caracterização e Análise Química

Dos efeitos da Procriação Medicamente Assistida no Direito Sucessório

Dissertação de mestrado em Direito das Crianças, Família e Sucessões

The role of macroH2A1 in prostate carcinogenesis

Dissertação de mestrado em Genética Molecular

Agentes deletéreos para Trypanosoma cruzi: Patogenia de la infección de placenta humana en la enfermedad congénita de Chagas, in vitro. Deleterious agents to Trypanosoma cruzi: Pathogenia of the human placenta infection in the congenital Chagas disease.

Trypanosoma cruzi, agente causal del Chagas, atraviesa la barrera placentaria y produce la enfermedad congénita. Objetivo general: Analizar si el T. cruzi, agente causal del Chagas, produce alteraciones trofoblásticas de las vellosidades coriónicas mediadas por óxido nítrico (principal agente deletéreo contra T. cruzi) y estrés oxidativo con variaciones que pudieran depender de la disponibiidad de L-arginine, sobre placentas en modelos in vitro de co-cultivos de explantos de vellosidades coriónicas, de sinciciotrofoblasto aislado y de células derivadas del trofoblasto de placentas humanas en interacción con distintas cepas del Trypanosoma cruzi, que pudieran dar alguna luz en la explicación de mecanismos involucrados en la infección placentaria y en algunos síndromes clínicos de la transmisión congénita del Chagas. Objetivos Específicos: a) Describir alteraciones estructurales y presencia de T. cruzi en vellosidades coriónicas de placentas humanas procedentes de co-cultivos con Trypanosoma cruzi in vitro (y sus respectivos controles), mediante técnicas histológicas y PCR analizando secuencias de ADN específicas del parásito.b) Establecer la localización y expresión proteica y la expresión transcripcional de las isoformas II y III de la Öxido Nítrico Sintasa sobre la misma población muestral de (a) mediante técnicas inmunohistoquímica, RT-PCR y semicuantificación con software adecuado. c) Analizar la susceptibilidad a la infección por el T. cruzi del citotrofoblasto (CTB) y sinciciotrofoblasto (STB) placentario aislado in vitro. d) Determinar concentraciones de óxido nítrico y estrés oxidativo del sinciciotrofoblasto (STB) aislado ante la infección por T. cruzi. e) Relacionar concentraciones de L-arginina con infección del trofoblasto aislado. f) Relacionar inhibiciones de la eNOS y de la arginasa con infección trofoblástica y óxido nítrico producido.Se emplearán métodos y técnicas de Biología celular y molecular, mediciones hormonales, enzimáticas, proteicas, parasitarias y bioquímicas en medios sobrenadantes de cultivo, de inmuno-detección de epitopes proteicos en tejidos, expresión de ARN por RT-PCR, Western blot, detección de DNA en tejidos por PCR, Cuantificaciones morfométricas. En general, el presente proyecto podría redundar en beneficios para un sector de la población de las áreas endémicas para esta enfermedad de bajos recursos económicos, sociales y culturales, mediante la obtención de datos que pudieran explicar algunos mecanismos de síndromes clínicos descriptos en esta patología y que pudieran participar en la transmisión congénita de la enfermedad de Chagas.

mRNA metabolism: nonsense mediated mRNA decay as a tool for gene therapy and the role of human DIS3L2 in transcript degradation

Tese de mestrado em Biologia Humana e Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015

Contribuição ao conhecimento das larvas dos Sarcophagidae com especial referência ao esqueleto cefálico (Diptera)

The author publishes a comparative study of eleven species of Sarcophagid flies and gives a redescription of the larval stages of Musca domestica L. as a model. The work was made upon material obtained from Sarcophagidae reared in the Laboratory. Some of them were parasitic flies from Insects and other invertebrates. Protodexia was reared using the domestic cockroach (Periplaneta americana) instead of the Orthroptera or Mantodea its true hosts. The larvae obtained by dissection of female abdomen was reared in flesh or agarhorse serum. The last proceeding is very good since the skins of all larval stages can be conserved for study and it is possible to observe the ecdyses. Some of the larvae prefer dead snails (Bulimulus and Fruticicola) and is able to destroy larvae of other species found in the same molluscs. The first stage maggot can be obtained by dissections of dried female specimens and furnishes very good characters to determine the species and establish the philogenetical relationship of the genera in the family. Th pseudocephalon presents very curious ornaments or grooves in some species (Oxysarcodexia). Sometimes there is a pigmented capsule covering a great part of the pseudocephalon (Titanogrypa). The cephaloskeletal sclerietes have a peculiar shape and constitution for every species, mainly in the first stage maggot.

Cosa: arqueologia de un enclave comercial mediterráneo. Campaña de 2006

En el marco del proyecto “La ciutat romana de Cosa: arqueologia d’un enclau comercial mediterrani” , autorizado y apoyado por la Soprintendenza Archeologica por la Toscana, entre los dias 4 y 22 de septiembre de 2006 se ha realizado la segunda campaña de intervenciones arqueológicas en la ciudad romana de Cosa (Ansedonia, prov. Grosseto, Itàlia), colonia latina fundada en el 273 aC a unos 120 km. al norte de Roma. De acuerdo a los resultados obtenidos en la campanya del 2005 (localización/verificación de los límites precisos de la ínsula O-P/4-5 mediante la aplicación de técnicas de prospección geofísica completadas con la limpieza, registro y documentación arqueológica de las estructuras localizadas ) los trabajos del 2006 se han orientado hacia la identificación de la organización interna de la dicha ínsula tomando como referente el criptopórtico situado en el extremo N.E., el cual parece constituir el límite de una estructura singular (privada o pública ) estratégicamente ubicada en relación al fórum i a la Via Sacra. El trabajo de campo ha consistido en un intenso decapage con la finalidad de delimitar unidades de habitación complejas funcionalmente definidas y así la articulación existente entre ellas; en este sentido se ha podido documentar evidencias del espacio porticado superpuesto al criptopórtico así como, paralelamente a la calle 5 y en dirección a la Via Sacra, parte de habitaciones algunas de las cuales conservaban restos del pavimiento original, en un caso de mosaico. Paralelamente, se ha realizado el análisis en laboratorio de los materiales recuperados los cuales, aún procediendo de nivel superficial, empiezan a proporcionar datos sobre los diferentes momentos de ocupación de la zona, básicamente tardorepublicanos y augustales.

Redirecció de l'especificitat de les cél·lules T contra epítops del VIH restringit per la HLA-A2 mitjaçant transferència genética

Existeixen creixents evidències què la resposta dels limfòcits T CD8+ alpha beta citotòxics (CTLs) és un element fonamental en la infecció produïda pel VIH. Les CTLs VIH especifiques es consideren molt importants en la reducció de la càrrega viral i en la contenció de la infecció. Encara que la combinació dels antiretrovirals (HAART) ha suposat una millora considerable en la lluita contra el VIH induint una important reducció de la càrrega viral i augmentant el nombre de cèl•lules T CD4+, diverses complicacions han fet ressaltar la necessitat de noves alternatives terapèutiques. Les complicacions inclouen: manca de recuperació d’una resposta immune sòlida contra el VIH, toxicitat a llarg termini de la teràpia i el descobriment que les cèl•lules T CD4+ constitueixen un reservori pel virus. Les noves alternatives controlaran la replicació viral i reconstituiran la immunitat. L’eficàcia de la immunoteràpia cel•lular amb transferència adoptiva de CTLs virals específics s’ha provat en diferents infeccions virals humanes, incloent el VIH. Proposem una modificació de la immunoteràpia adoptiva redirigint l’especificitat de les cèl•lules T contra el VIH mitjançant la transfecció dels gens del TCR. En aquest assaig preclínic, ens aprofitarem de la tecnologia dels animals transgènics per les molècules de HLA, amb la finalitat de generar TCRs d’alta afinitat dirigits contra epitops del VIH restringits per la molècula HLA. Aquests TCRs seran induïts in vivo i seleccionats in vitro. Les cadenes alpha i beta dels TCRs VIH específics procedents de les CTLs seran clonades mitjançant tècniques de biologia molecular. Aquests TCRs VIH específics seran transferits a cèl•lules T CD8+ humanes i la seva especificitat i capacitat citolítica contra cèl•lules diana que presentin antígens de VIH-1 s’estudiaran mitjançant la combinació de diverses tècniques noves (FCC, transfecció mitjançant Nucleoefector). Finalment, una construcció retroviral adient per la seva transducció en cèl•lules T humanes s’establirà amb un TCR òptim seleccionat.

Melanoma patients respond to a cytotoxic T lymphocyte-defined self-peptide with diverse and nonoverlapping T-cell receptor repertoires.

HLA-A2+ melanoma patients develop naturally a strong CD8+ T cell response to a self-peptide derived from Melan-A. Here, we have used HLA-A2/peptide tetramers to isolate Melan-A-specific T cells from tumor-infiltrated lymph nodes of two HLA-A2+ melanoma patients and analyzed their TCR beta chain V segment and complementarity determining region 3 length and sequence. We found a broad diversity in Melan-A-specific immune T-cell receptor (TCR) repertoires in terms of both TCR beta chain variable gene segment usage and clonal composition. In addition, immune TCR repertoires selected in the patients were not overlapping. In contrast to previously characterized CD8+ T-cell responses to viral infections, this study provides evidence against usage of highly restricted TCR repertoire in the natural response to a self-differentiation tumor antigen.

Differential effects of two anti-apo-cytochrome c-specific monoclonal antibodies on the function of apo-cytochrome c-specific murine T cell clones.

A murine monoclonal antibody (SJL 2-4) specific for the antigen apo-cytochrome c was shown to inhibit both antigen-induced proliferation and lymphokine secretion by an apo-cytochrome c-specific BALB/c helper T cell clone. The inhibition was specific because additional apo-cytochrome c-specific T cell clones were not inhibited by the same monoclonal antibody. Time course studies of the inhibition indicated that the initial 8 hr of contact between T cell clones and antigen-presenting cells were critical for activation of the T cell clones. Inhibition of T cell functions by antigen-specific antibodies appeared to correlate with the antibody-antigen binding constant because a second monoclonal antibody (Cyt-1-59), with identical specificity but with a lower affinity constant for apo-cytochrome c, had very little inhibitory effect on the proliferation or lymphokine secretion of apo-cytochrome c-specific T cell clones.

Structure-function relationships of the alpha1b-adrenergic receptor.

The alpha1b-adrenergic receptor (AR) is a member of the large superfamily of seven transmembrane domain (TMD) G protein-coupled receptors (GPCR). Combining site-directed mutagenesis of the alpha1b-AR with computational simulations of receptor dynamics, we have explored the conformational changes underlying the process of receptor activation, i.e. the transition between the inactive and active states. Our findings suggest that the structural constraint stabilizing the alpha1b-AR in the inactive form is a network of H-bonding interactions amongst conserved residues forming a polar pocket and R143 of the DRY sequence at the end of TMDIII. We have recently reported that point mutations of D142, of the DRY sequence and of A293 in the distal portion of the third intracellular loop resulted in ligand-independent (constitutive) activation of the alpha1b-AR. These constitutively activating mutations could induce perturbations resulting in the shift of R143 out of the polar pocket. The main role of R143 may be to mediate receptor activation by triggering the exposure of several basic amino acids of the intracellular loops towards the G protein. Our investigation has been extended also to the biochemical events involved in the desensitization process of alpha1b-AR. Our results indicate that immediately following agonist-induced activation, the alpha1b-AR can undergo rapid agonist-induced phosphorylation and desensitization. Different members of the G protein coupled receptor kinase family can play a role in agonist-induced regulation of the alpha1b-AR. In addition, constitutively active alpha1b-AR mutants display different phosphorylation and internalization features. The future goal is to further elucidate the molecular mechanism underlying the complex equilibrium between activation and inactivation of the alpha1b-AR and its regulation by pharmacological substances. These findings can help to elucidate the mechanism of action of various agents displaying properties of agonists or inverse agonists at the adrenergic system.

Redirection of T cells by delivering a transgenic mouse-derived MDM2 tumor antigen-specific TCR and its humanized derivative is governed by the CD8 coreceptor and affects natural human TCR expression.

Retroviral transfer of T cell antigen receptor (TCR) genes selected by circumventing tolerance to broad tumor- and leukemia-associated antigens in human leukocyte antigen (HLA)-A*0201 (A2.1) transgenic (Tg) mice allows the therapeutic reprogramming of human T lymphocytes. Using a human CD8 x A2.1/Kb mouse derived TCR specific for natural peptide-A2.1 (pA2.1) complexes comprising residues 81-88 of the human homolog of the murine double-minute 2 oncoprotein, MDM2(81-88), we found that the heterodimeric CD8 alpha beta coreceptor, but not normally expressed homodimeric CD8 alpha alpha, is required for tetramer binding and functional redirection of TCR- transduced human T cells. CD8+T cells that received a humanized derivative of the MDM2 TCR bound pA2.1 tetramers only in the presence of an anti-human-CD8 anti-body and required more peptide than wild-type (WT) MDM2 TCR+T cells to mount equivalent cytotoxicity. They were, however, sufficiently effective in recognizing malignant targets including fresh leukemia cells. Most efficient expression of transduced TCR in human T lymphocytes was governed by mouse as compared to human constant (C) alphabeta domains, as demonstrated with partially humanized and murinized TCR of primary mouse and human origin, respectively. We further observed a reciprocal relationship between the level of Tg WT mouse relative to natural human TCR expression, resulting in T cells with decreased normal human cell surface TCR. In contrast, natural human TCR display remained unaffected after delivery of the humanized MDM2 TCR. These results provide important insights into the molecular basis of TCR gene therapy of malignant disease.

A glycine-arginine domain in control of the human MRE11 DNA repair protein.

Human MRE11 is a key enzyme in DNA double-strand break repair and genome stability. Human MRE11 bears a glycine-arginine-rich (GAR) motif that is conserved among multicellular eukaryotic species. We investigated how this motif influences MRE11 function. Human MRE11 alone or a complex of MRE11, RAD50, and NBS1 (MRN) was methylated in insect cells, suggesting that this modification is conserved during evolution. We demonstrate that PRMT1 interacts with MRE11 but not with the MRN complex, suggesting that MRE11 arginine methylation occurs prior to the binding of NBS1 and RAD50. Moreover, the first six methylated arginines are essential for the regulation of MRE11 DNA binding and nuclease activity. The inhibition of arginine methylation leads to a reduction in MRE11 and RAD51 focus formation on a unique double-strand break in vivo. Furthermore, the MRE11-methylated GAR domain is sufficient for its targeting to DNA damage foci and colocalization with gamma-H2AX. These studies highlight an important role for the GAR domain in regulating MRE11 function at the biochemical and cellular levels during DNA double-strand break repair.

NR2E3 mutations in enhanced S-cone sensitivity syndrome (ESCS), Goldmann-Favre syndrome (GFS), clumped pigmentary retinal degeneration (CPRD), and retinitis pigmentosa (RP).

NR2E3, also called photoreceptor-specific nuclear receptor (PNR), is a transcription factor of the nuclear hormone receptor superfamily whose expression is uniquely restricted to photoreceptors. There, its physiological activity is essential for proper rod and cone photoreceptor development and maintenance. Thirty-two different mutations in NR2E3 have been identified in either homozygous or compound heterozygous state in the recessively inherited enhanced S-cone sensitivity syndrome (ESCS), Goldmann-Favre syndrome (GFS), and clumped pigmentary retinal degeneration (CPRD). The clinical phenotype common to all these patients is night blindness, rudimental or absent rod function, and hyperfunction of the "blue" S-cones. A single p.G56R mutation is inherited in a dominant manner and causes retinitis pigmentosa (RP). We have established a new locus-specific database for NR2E3 (www.LOVD.nl/eye), containing all reported mutations, polymorphisms, and unclassified sequence variants, including novel ones. A high proportion of mutations are located in the evolutionarily-conserved DNA-binding domains (DBDs) and ligand-binding domains (LBDs) of NR2E3. Based on homology modeling of these NR2E3 domains, we propose a structural localization of mutated residues. The high variability of clinical phenotypes observed in patients affected by NR2E3-linked retinal degenerations may be caused by different disease mechanisms, including absence of DNA-binding, altered interactions with transcriptional coregulators, and differential activity of modifier genes.