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.

FTIR, a potential tool to dementia diagnosis trough analysis of plasma

Nowadays it is still difficult to perform an early and accurate diagnosis of dementia, therefore many research focus on the finding of new dementia biomarkers that can aid in that purpose. So scientists try to find a noninvasive, rapid, and relatively inexpensive procedures for early diagnosis purpose. Several studies demonstrated that the utilization of spectroscopic techniques, such as Fourier Transform Infrared Spectroscopy (FTIR) and Raman spectroscopy could be an useful and accurate procedure to diagnose dementia. As several biochemical mechanisms related to neurodegeneration and dementia can lead to changes in plasma components and others peripheral body fluids, blood-based samples and spectroscopic analyses can be used as a more simple and less invasive technique. This work is intended to confirm some of the hypotheses of previous studies in which FTIR was used in the study of plasma samples of possible patient with AD and respective controls and verify the reproducibility of this spectroscopic technique in the analysis of such samples. Through the spectroscopic analysis combined with multivariate analysis it is possible to discriminate controls and demented samples and identify key spectroscopic differences between these two groups of samples which allows the identification of metabolites altered in this disease. It can be concluded that there are three spectral regions, 3500-2700 cm -1, 1800-1400 cm-1 and 1200-900 cm-1 where it can be extracted relevant spectroscopic information. In the first region, the main conclusion that is possible to take is that there is an unbalance between the content of saturated and unsaturated lipids. In the 1800-1400 cm-1 region it is possible to see the presence of protein aggregates and the change in protein conformation for highly stable parallel β-sheet. The last region showed the presence of products of lipid peroxidation related to impairment of membranes, and nucleic acids oxidative damage. FTIR technique and the information gathered in this work can be used in the construction of classification models that may be used for the diagnosis of cognitive dysfunction.

Desenvolvimento de metodologias alternativas para quantificação de micronutrientes em produtos de nutrição infantil

As farinhas infantis, alimentos que se destinam a recém-nascidos e crianças até à idade pré-escolar, devem satisfazer todas as necessidades nutricionais que se verificam durante o período de crescimento e desenvolvimentos físico e mental desta faixa etária. Desta forma, são frequentemente adicionadas prémisturas de vitaminas e minerais durante a sua produção (fortificação), de maneira a que a quantidade adicionada e a composição do produto final sejam concordantes com a legislação comunitária em vigor. A implementação, na linha de produção, de métodos alternativos de análise “amigos do ambiente” e passíveis de obter resultados rápidos acerca da composição nutricional dos produtos alimentares, mesmo antes destes serem embalados, permite reduções de tempo, custos e um melhor controlo do processo de produção. A espectroscopia FT-NIR e a espectroscopia de XRF são técnicas que permitem a quantificação de micronutrientes e possuem características fundamentais ao controlo rápido de processos. Neste trabalho foram desenvolvidos modelos de calibração para quantificação de zinco, por espectroscopia de XRF, em três receitas de pré-misturas de vitaminas e minerais. Construíram-se dois modelos de calibração, um com um R2 de 0,990 e um SEC de 26,624 mg/100g e outro com um R2 de 0,927 e um SEC de 18,838 mg/100g. Estes resultados indicam que os modelos de calibração construídos são adequados e podem ser usados na determinação rápida do teor de zinco em pré-misturas de vitaminas e minerais. Foram também verificadas as rectas de calibração existentes para quantificação de cálcio e ferro por espectroscopia de XRF e quantificação de vitamina C por espectroscopia FT-NIR para aplicação nas novas receitas de pré-misturas de vitaminas e minerais.