Protemic characterization of peripheral blood mononuclear cells

Peripheral blood mononuclear cells (PBMCs) play quite diverse and important roles in monitoring immune homeostasis. Thus, these subset of blood cells may provide access to potential physiological relevant biomolecules, namely proteins. For this reason, PBMCs represent a promising biological sample in scientific research, particularly as a source of potential biological markers discovery of the most diverse diseases. Prior studies of proteomic characterization of PBMCs from healthy individuals lack either the identification of a large number of proteins or its quantification in a way that is compatible with the search of potential biomarker candidates. Therefore, this study aimed to provide a comprehensive PBMCs proteome characterisation as well as to create a SWATH library. It was also evaluated if by using the BD Vacutainer® CPT™ tubes for PBMCs isolation, it would be possible to identify a larger number of immunologically relevant proteins in comparison to plasma samples. The enrichment test assay revealed that it is possible to identify more immune-related proteins from isolated PBMCs than from plasma. Moreover, the majority of the quantified proteins with an “immune system” GO term assigned is present in higher amounts in PBMCs samples. 2D LC-MS/MS proved to be the best approach to use in qualitative analysis of PBMCs and in the construction of a SWATH library, since it resulted in an increase of both identified and quantified proteins (66.3% and 16.9%, respectively) in comparison to 1D LC-MS/MS. A total of 2071 proteins were identified and it was possible to quantify 922 different proteins among six distinct samples. From these proteins, 445 were commom between all individuals. In conclusion, this work provides a comprehensive PBMCs proteome dataset that will be useful in further studies that focus on the search for potential biological markers of various pathologies in these cells. Additionally, SWATH-MS proved to be a reproducible and effective acquisition method to quantify PBMCs proteins.

Study of tRNA modifying enzymes and codon usage bias in cancer

Recent evidences indicate that tRNA modifications and tRNA modifying enzymes may play important roles in complex human diseases such as cancer, neurological disorders and mitochondrial-linked diseases. We postulate that expression deregulation of tRNA modifying enzymes affects the level of tRNA modifications and, consequently, their function and the translation efficiency of their tRNA corresponding codons. Due to the degeneracy of the genetic code, most amino acids are encoded by two to six synonymous codons. This degeneracy and the biased usage of synonymous codons cause alterations that can span from protein folding to enhanced translation efficiency of a select gene group. In this work, we focused on cancer and performed a meta-analysis study to compare microarray gene expression profiles, reported by previous studies and evaluate the codon usage of different types of cancer where tRNA modifying enzymes were found de-regulated. A total of 36 different tRNA modifying enzymes were found de-regulated in most cancer datasets analyzed. The codon usage analysis revealed a preference for codons ending in AU for the up-regulated genes, while the down-regulated genes show a preference for GC ending codons. Furthermore, a PCA biplot analysis showed this same tendency. We also analyzed the codon usage of the datasets where the CTU2 tRNA modifying enzyme was found deregulated as this enzyme affects the wobble position (position 34) of specific tRNAs. Our data points to a distinct codon usage pattern between up and downregulated genes in cancer, which might be caused by the deregulation of specific tRNA modifying enzymes. This codon usage bias may augment the transcription and translation efficiency of some genes that otherwise, in a normal situation, would be translated less efficiently.

Modificação da pasta kraft de eucalipto para novas aplicações

Este trabalho constou num estudo da modificação da pasta kraft de eucalipto, utilizando uma técnica de processamento por alta pressão hidrostática com o intuito de melhorar a sua performance para novas aplicações tal como o papel tissue ou o papel para embalagens. Para tal pretendia-se melhorar algumas propriedades da pasta com a utilização da técnica de alta pressão hidrostática. Realizou-se um estudo preliminar onde se submeteu uma pasta branqueada A, não refinada, a um tratamento hiperbárico (TH) numa gama de pressões de 5000-8000 bar. Para uma pressão de 6000 bar constatou-se uma melhoria de cerca de 16 % no alongamento percentual na rotura, 17 % na resistência à tração, 27 % no índice de rebentamento e cerca de 19 % no índice de rasgamento. Posteriormente, e tendo em conta os resultados positivos verificados na pasta A, estudou-se o efeito do TH numa pasta branqueada B variando a consistência de tratamento (1,5% ou 3%) e o tempo de processamento (5 ou 10 minutos). Foi estudado também o efeito do TH quando aplicado antes e após a refinação da pasta. A pasta branca foi submetida à refinação num moinho PFI entre 1000 e 3000 rotações. Os resultados obtidos mostram que o TH realizado a menores consistências apresenta um efeito mais significativo nas propriedades físico-mecânicas de pastas e que o efeito é distinto quando o processamento é aplicado antes e depois da refinação, tendo-se registado melhoramentos das propriedades mecânicas apenas quando o TH ocorre após a refinação. A pasta kraft foi também modificada com anidrido alquenil succínico (ASA). A modificação da pasta de celulose com ASA resultou numa diminuição das propriedades mecânicas e para além disso não gerou qualquer alteração na termoplasticidade do material, no entanto registou-se um aumento na resistência à molhabilidade. Concluiu-se que o TH conduz a alterações ao nível de propriedades mecânicas e estruturais da pasta de interesse para a aplicação em papéis tissue no caso da pasta B. Para além disso a modificação da pasta com ASA resultou em alterações de interesse particular para papéis de embalagem.