Entropy analysis of DNA code dynamics in human chromosomes

Deoxyribonucleic acid, or DNA, is the most fundamental aspect of life but present day scientific knowledge has merely scratched the surface of the problem posed by its decoding. While experimental methods provide insightful clues, the adoption of analysis tools supported by the formalism of mathematics will lead to a systematic and solid build-up of knowledge. This paper studies human DNA from the perspective of system dynamics. By associating entropy and the Fourier transform, several global properties of the code are revealed. The fractional order characteristics emerge as a natural consequence of the information content. These properties constitute a small piece of scientific knowledge that will support further efforts towards the final aim of establishing a comprehensive theory of the phenomena involved in life.

Shannon, rényie and tsallis entropy analysis of DNA using phase plane

This paper analyzes DNA information using entropy and phase plane concepts. First, the DNA code is converted into a numerical format by means of histograms that capture DNA sequence length ranging from one up to ten bases. This strategy measures dynamical evolutions from 4 up to 410 signal states. The resulting histograms are analyzed using three distinct entropy formulations namely the Shannon, Rényie and Tsallis definitions. Charts of entropy versus sequence length are applied to a set of twenty four species, characterizing 486 chromosomes. The information is synthesized and visualized by adapting phase plane concepts leading to a categorical representation of chromosomes and species.

Fractional dynamics in DNA

This paper addresses the DNA code analysis in the perspective of dynamics and fractional calculus. Several mathematical tools are selected to establish a quantitative method without distorting the alphabet represented by the sequence of DNA bases. The association of Gray code, Fourier transform and fractional calculus leads to a categorical representation of species and chromosomes.

Wavelet analysis of human DNA

This paper studies the human DNA in the perspective of signal processing. Six wavelets are tested for analyzing the information content of the human DNA. By adopting real Shannon wavelet several fundamental properties of the code are revealed. A quantitative comparison of the chromosomes and visualization through multidimensional and dendograms is developed.

Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

On the DNA of eleven mammals

This paper studies the DNA code of eleven mammals from the perspective of fractional dynamics. The application of Fourier transform and power law trendlines leads to a categorical representation of species and chromosomes. The DNA information reveals long range memory characteristics.

Multi-dimensional scaling applied to histogram-based DNA analysis

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method’s artifacts.

A DNA barcode approach of the Laurencia complex (Ceramiales, Rodophyta) in the tropical and subtropical Atlantic ocean

10th International Phycological Congress, Orlando, Florida, USA, 4-10 de agosto 2013.

DNA-barcoding revela la existencia de un posible nuevo género del complejo Laurencia (Rodophyta, Ceramiales) en las islas Canarias

XIX Simposio de Botánica Criptogámica, Las Palmas de Gran Canaria, 24-28 de junio de 2013.

Efeitos da ingestão de simbiótico e indol-3-carbinol sobre o processo de carcinogênese química de cólon em ratos Wistar alimentados com dieta contendo heme

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hydrogen peroxide sensing, signaling and regulation of transcription factors

The regulatory mechanisms by which hydrogen peroxide (H2O2) modulates the activity of transcription factors in bacteria (OxyR and PerR), lower eukaryotes (Yap1, Maf1, Hsf1 and Msn2/4) and mammalian cells (AP-1, NRF2, CREB, HSF1, HIF-1, TP53, NF-κB, NOTCH, SP1 and SCREB-1) are reviewed. The complexity of regulatory networks increases throughout the phylogenetic tree, reaching a high level of complexity in mammalians. Multiple H2O2 sensors and pathways are triggered converging in the regulation of transcription factors at several levels: (1) synthesis of the transcription factor by upregulating transcription or increasing both mRNA stability and translation; (ii) stability of the transcription factor by decreasing its association with the ubiquitin E3 ligase complex or by inhibiting this complex; (iii) cytoplasm-nuclear traffic by exposing/masking nuclear localization signals, or by releasing the transcription factor from partners or from membrane anchors; and, (iv) DNA binding and nuclear transactivation by modulating transcription factor affinity towards DNA, co-activators or repressors, and by targeting specific regions of chromatin to activate individual genes. We also discuss how H2O2 biological specificity results from diverse thiol protein sensors, with different reactivity of their sulfhydryl groups towards H2O2, being activated by different concentrations and times of exposure to H2O2. The specific regulation of local H2O2 concentrations is also crucial and results from H2O2 localized production and removal controlled by signals. Finally, we formulate equations to extract from typical experiments quantitative data concerning H2O2 reactivity with sensor molecules. Rate constants of 140 M-1s−1 and ≥ 1.3 × 103 M-1s−1 were estimated, respectively, for the reaction of H2O2 with KEAP1 and with an unknown target that mediates NRF2 protein synthesis. In conclusion, the multitude of H2O2 targets and mechanisms provides an opportunity for highly specific effects on gene regulation that depend on the cell type and on signals received from the cellular microenvironment.

Depleção do DNA mitocondrial (mtDNA) em leucócitos de doentes com doença Machado-Joseph : um estudo piloto

Dissertação de Mestrado, Ciências Biomédicas, 5 de Outubro de 2015, Universidade dos Açores.

Hélices e Espirais em Micro e Nanofibras Celulósicas

A celulose é o polímero renovável mais abundante do mundo. É conhecido pela sua excelente biocompatibilidade, propriedades térmicas e mecânicas. A celulose assim como os polipéptideos e o ADN, pertence a uma família de moléculas orgânicas que dão origem à formação de fases líquidas cristalinas (LCs) colestéricas. A Passiflora Edulis, tal como outras plantas trepadeiras, possui longas e flexíveis gavinhas que permitem à planta encontrar um suporte para se fixar. As gavinhas podem assumir a forma de espirais ou de hélices consoante sejam sustentadas por apenas uma ou por ambas as extremidades. As hélices apresentam muitas vezes duas porções helicoidais, uma esquerda e outra direita, separadas por um segmento recto denominado perversão. Este comportamento é consequência da curvatura intrínseca das gavinhas produzidas pela planta trepadeira. O mesmo comportamento pode ser observado em micro e nanofibras celulósicas fabricadas a partir de soluções líquido-cristalinas, numa escala três a quatro ordens de grandeza inferior à das gavinhas. Este facto sugere que o modelo físico utilizado tenha invariância de escala. Neste trabalho é feito o estudo de fibras e jactos que imitam as estruturas helicoidais apresentadas pelas gavinhas das plantas trepadeiras. As fibras e jactos são produzidos a partir de soluções líquidas cristalinas celulósicas. De modo a determinar as características morfológicas e estruturais, que contribuem para a curvatura das fibras, foram utilizadas técnicas de imagem por ressonância magnética (MRI), microscopia óptica com luz polarisada (MOP), microscopia electrónica de varrimento (SEM) e microscopia de força atómica (AFM) . A variação da forma das estruturas helicoidais com a temperatura parece ser relevante para o fabrico de membranas não tecidas para aplicação em sensores termo-mecânicos.

Comparação de métodos de extração de DNA e deteção de organismos geneticamente modificados em alimentos processados derivados de milho

Diante dos avanços biotecnológicos o cultivo de plantas geneticamente modificadas, como, por exemplo, o milho (Zea mays), aumentou consideravelmente nos últimos anos. Embora esta tecnologia apresente comprovados benefícios em relação ao aumento da produtividade e durabilidade do alimento, a população ainda receia em consumir produtos geneticamente modificados. O objetivo deste trabalho foi comparar dois protocolos baseados na utilização de CTAB e avaliar qual o melhor para extração de DNA em alimentos processados derivados de milho, bem como identificar dois dos resíduos transgênicos mais comuns em gêneros alimentícios derivados de milho: Cry1ab e Cry1F. Para isto, 14 amostras derivadas de milho foram avaliadas utilizando dois diferentes protocolos de extração de DNA e a deteção dos eventos transgênicos conduzida pela técnica de PCR qualitativa. Entre as amostras analisadas, 57% resultaram positivas para deteção de ambos os eventos de milho transgênico avaliados.

Detecção de DNA de Leishmania braziliensis em pacientes de leishmaniose tegumentar americana

Foi realizado diagnóstico para leishmaniose tegumentar americana a partir de sangue de pacientes residentes em dois municípios endêmicos do estado de Pernambuco. O DNA de 119 amostras de sangue foi extraído e submetido a reação em cadeia da polimerase. Utilizaram-se primers do minicírculo do DNA do cinetoplasto (kDNA) de Leishmania braziliensis, circulante em Pernambuco, cuja seqüência-alvo gera um fragmento de 750 pares de bases. No total 58 (48,7%) indivíduos apresentaram amplificação positiva e 61 (51,3%) negativa. Das amostras positivas para a PCR, 37 (≅ 64%) pertenciam a indivíduos tratados e sem lesão. Conclui-se que a técnica de PCR é eficaz para identificar o DNA de leishmânia em material de biópsias e em sangue venoso.