Can power laws help us understand gene and proteome information?

Proteins are biochemical entities consisting of one or more blocks typically folded in a 3D pattern. Each block (a polypeptide) is a single linear sequence of amino acids that are biochemically bonded together. The amino acid sequence in a protein is defined by the sequence of a gene or several genes encoded in the DNA-based genetic code. This genetic code typically uses twenty amino acids, but in certain organisms the genetic code can also include two other amino acids. After linking the amino acids during protein synthesis, each amino acid becomes a residue in a protein, which is then chemically modified, ultimately changing and defining the protein function. In this study, the authors analyze the amino acid sequence using alignment-free methods, aiming to identify structural patterns in sets of proteins and in the proteome, without any other previous assumptions. The paper starts by analyzing amino acid sequence data by means of histograms using fixed length amino acid words (tuples). After creating the initial relative frequency histograms, they are transformed and processed in order to generate quantitative results for information extraction and graphical visualization. Selected samples from two reference datasets are used, and results reveal that the proposed method is able to generate relevant outputs in accordance with current scientific knowledge in domains like protein sequence/proteome analysis.

Cellular hypomethylation is associated with impaired nitric oxide production by cultured human endothelial cells

Hyperhomocysteinemia (HHcy) is a risk factor for vascular disease, but the underlying mechanisms remain incompletely defined. Reduced bioavailability of nitric oxide (NO) is a principal manifestation of underlying endothelial dysfunction, which is an initial event in vascular disease. Inhibition of cellular methylation reactions by S-adenosylhomocysteine (AdoHcy), which accumulates during HHcy, has been suggested to contribute to vascular dysfunction. However, thus far, the effect of intracellular AdoHcy accumulation on NO bioavailability has not yet been fully substantiated by experimental evidence. The present study was carried out to evaluate whether disturbances in cellular methylation status affect NO production by cultured human endothelial cells. Here, we show that a hypomethylating environment, induced by the accumulation of AdoHcy, impairs NO production. Consistent with this finding, we observed decreased eNOS expression and activity, but, by contrast, enhanced NOS3 transcription. Taken together, our data support the existence of regulatory post-transcriptional mechanisms modulated by cellular methylation potential leading to impaired NO production by cultured human endothelial cells. As such, our conclusions may have implications for the HHcy-mediated reductions in NO bioavailability and endothelial dysfunction.

Compostos de dextrano-manose marcados com o 67Ga para a deteção do gânglio sentinela

Mestrado em Medicina Nuclear - Área de especialização: Radiofarmácia.

Pesquisa de péptidos em Macroalgas dos Açores com potencial atividade inibitória da Enzima Conversora da Angiotensina I (ECA): Extração, purificação, caracterização e avaliação da sua atividade anti-hipertensiva

Jornadas "Ciência nos Açores – que futuro? Tema Ciências Naturais e Ambiente", Ponta Delgada, 7-8 de Junho de 2013.

Edible Azorean macroalgae as source of rich nutrients with impact on human health

Copyright © 2014 Elsevier Ltd. All rights reserved.

Desenvolvimento de tecnologias de extração e de quantificação dos principais componentes nutricionais de macroalgas do litoral dos Açores tendo em vista o seu aproveitamento como suplemento alimentar

Dissertação de Mestrado em Tecnologia e Segurança Alimentar

Sequencing of a 9.9 kb segment on the right arm of yeast chromosome VII reveals four open reading frames, including PFK1, the gene coding for succinyl-CoA synthetase (beta-chain) and two ORFs sharing homology with ORFs of the yeast chromosome VIII

A 9.9 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains four open reading frames (ORFs) longer than 100 amino acids. One gene, PFK1, has already been cloned and sequenced and the other one is the probable yeast gene coding for the beta-subunit of the succinyl-CoA synthetase. The two remaining ORFs share homology with the deduced amino acid sequence (and their physical arrangement is similar to that) of the YHR161c and YHR162w ORFs from chromosome VIII.

Sequencing of a 17.6 kb segment on the right arm of yeast chromosome VII reveals 12 ORFs, including CCT, ADE3 and TR-I genes, homologues of the yeast PMT and EF1G genes, of the human and bacterial electron-transferring flavoproteins (beta-chain) and of the Escherichia coli phosphoserine phosphohydrolase, and five new ORFs.

A 17.6 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains twelve open reading frames (ORFs) longer than 100 amino acids. Three genes had already been cloned and sequenced: CCT, ADE3 and TR-I. Two ORFs are similar to other yeast genes: G7722 with the YAL023 (PMT2) and PMT1 genes, encoding two integral membrane proteins, and G7727 with the first half of the genes encoding elongation factors 1gamma, TEF3 and TEF4. Two other ORFs, G7742 and G7744, are most probably yeast orthologues of the human and Paracoccus denitrificans electron-transferring flavoproteins (beta chain) and of the Escherichia coli phosphoserine phosphohydrolase. The five remaining identified ORFs do not show detectable homology with other protein sequences deposited in data banks. The sequence has been deposited in the EMBL data library under Accession Number Z49133.

The periodic table: contest and exhibition

The systemization and organization of ideas and concepts is an integral part of science. In chemistry, the organization of the periodic table of the chemical elements in the 1860s was one of the greatest scientific breakthroughs ever made and in fact during the 20th century it became a universally recognized scientific icon (1). The periodic table is the fundamental classificatory scheme of the elements and summarizes the realm of chemistry (2). Simply knowing the position of an element in the periodic table tells us about its properties and is usually enough to predict how the element will behave in a wide variety of different situations or reactions (1). Based on this potential mine of information, it is possible to make reliable predictions of the properties of the compounds that each element forms. Nowadays, the concept of the periodic table is starting to interact with other sciences and reports of periodic tables of amino acids (3), genetic codes (4), protein structures (5), and biology (6) can be found in the specialized literature. Symbiosis between science and art, for example, “The Periodic Table of The Elephants” (7), can also be seen. To appeal to a better understanding of the periodic table, the Instituto Superior de Engenharia do Instituto Politécnico do Porto and the Centro de Química da Universidade do Porto promoted a contest and exhibit with the goal of stimulating a wide and heterogeneous audience, ranging from young children and their parents to graduate students from several disciplines, to explore the nature of this icon. Imaginative educational activities such as contests (8–10), games (11, 12), and puzzles (13–15) provided a way to communicate with the general public with the goal of attracting students to science. This also constituted an interesting, informative, and entertaining alternative to non-interactive lectures. Simultaneously, artistic creativity was combined with scientific knowledge.

Spectroscopic characterization of a novel 2 /[4Fe /4S] ferredoxin isolated from Desulfovibrio desulfuricans ATCC 27774

Inorganica Chimica Acta 356 (2003) 215-221

Evaluation of the role of glutathione in the lead-induced toxicity in saccharomyces cerevisiae

The effect of intracellular reduced glutathione (GSH) in the lead stress response of Saccharomyces cerevisiae was investigated. Yeast cells exposed to Pb, for 3 h, lost the cell proliferation capacity (viability) and decreased intracellular GSH level. The Pb-induced loss of cell viability was compared among yeast cells deficient in GSH1 (∆gsh1) or GSH2 (∆gsh2) genes and wild-type (WT) cells. When exposed to Pb, ∆gsh1 and ∆gsh2 cells did not display an increased loss of viability, compared with WT cells. However, the depletion of cellular thiols, including GSH, by treatment of WT cells with iodoacetamide (an alkylating agent, which binds covalently to thiol group), increased the loss of viability in Pb-treated cells. In contrast, GSH enrichment, due to the incubation of WT cells with amino acids mixture constituting GSH (l-glutamic acid, l-cysteine and glycine), reduced the Pb-induced loss of proliferation capacity. The obtained results suggest that intracellular GSH is involved in the defence against the Pb-induced toxicity; however, at physiological concentration, GSH seems not to be sufficient to prevent the Pb-induced loss of cell viability.

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon.

Nucleic Acid Research (2007) Vol.37 N. 14 4755-4766

Functional domains of Bacillus subtilis transcription factor AraR and identification of aminoacids important for nucleoprotein complex assembly and effector-binding.

Journal of Bacteriology (Apr 2006) 3024-3036

Characteristics of IEF, SDS and SAR-PAGE of Cuba EPO biosimilar

EPO is a glycoprotein produced in the kidney, which stimulates the division and differentiation of red cells in the bone marrow. Erythropoietin is available as a therapeutic agent produced by recombinant DNA technology in mammalian cell culture into which the human EPO gene has been transfected. Biosimilar Epoetins are mostly erythropoietins of the Epoetin alfa, beta or omega type, which are being produced at much lower cost due to expired patents. Recombinant human erythropoietin (rh-EPO) contains the identical amino acid sequence of natural EPO: 165 amino acids, with a molecular weight of 30,400 Da. Since glycosylation is not only dependent on the cell-line used for the expression of Epoetins but also on the entire biotechnological process the glycosylation patterns of biosimilars do not necessarily reflect the patterns of the originator compounds. Today biosimilar Epoetins are manufactured and distributed worldwide and under many different names. The use of recombinant EPOs for doping is prohibited because of its performance enhancing effect. The aim of the present study was to investigated whether biosimilar alpha r-HuEPO – ior®-EPOCIM, produced in Cuba and also available in other countries in all continents, could be differentiated from endogenous one by iso-electro-focusing plus double blotting, SDS-PAGE and SAR-PAGE for antidoping analysis.

Multiple sequence alignment correction using constraints

Trabalho apresentado no âmbito do European Master in Computational Logics, como requisito parcial para obtenção do grau de Mestre em Computational Logics