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.

Immunogenicity of WHO-17D and Brazilian 17DD yellow fever vaccines: a randomized trial

OBJECTIVE: To compare the immunogenicity of three yellow fever vaccines from WHO-17D and Brazilian 17DD substrains (different seed-lots). METHODS: An equivalence trial was carried out involving 1,087 adults in Rio de Janeiro. Vaccines produced by Bio-Manguinhos, Fiocruz (Rio de Janeiro, Brazil) were administered following standardized procedures adapted to allow blocked randomized allocation of participants to coded vaccine types (double-blind). Neutralizing yellow fever antibody titters were compared in pre- and post-immunization serum samples. Equivalence was defined as a difference of no more than five percentage points in seroconversion rates, and ratio between Geometric Mean Titters (GMT) higher than 0.67. RESULTS: Seroconversion rates were 98% or higher among subjects previously seronegative, and 90% or more of the total cohort of vaccinees, including those previously seropositive. Differences in seroconversion ranged from -0.05% to -3.02%. The intensity of the immune response was also very similar across vaccines: 14.5 to 18.6 IU/mL. GMT ratios ranged from 0.78 to 0.93. Taking the placebo group into account, the vaccines explained 93% of seroconversion. Viremia was detected in 2.7% of vaccinated subjects from Day 3 to Day 7. CONCLUSIONS: The equivalent immunogenicity of yellow fever vaccines from the 17D and 17DD substrains was demonstrated for the first time in placebo-controlled double-blind randomized trial. The study completed the clinical validation process of a new vaccine seed-lot, provided evidence for use of alternative attenuated virus substrains in vaccine production for a major manufacturer, and for the utilization of the 17DD vaccine in other countries.

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.

Reactogenicity of yellow fever vaccines in a randomized, placebo-controlled trial

OBJECTIVE: To compare the reactogenicity of three yellow fever (YF) vaccines from WHO-17D and Brazilian 17DD substrains (different seed-lots) and placebo. METHODS: The study involved 1,087 adults eligible for YF vaccine in Rio de Janeiro, Brazil. Vaccines produced by Bio-Manguinhos, Fiocruz (Rio de Janeiro, Brazil) were administered ("day 0") following standardized procedures adapted to allow blinding and blocked randomization of participants to coded vaccine types. Adverse events after immunization were ascertained in an interview and in diary forms filled in by each participant. Liver enzymes were measured on days 0, 4-20 and 30 of the study. Viremia levels were measured on days 4 to 20 of follow-up. The immune response was verified through serologic tests. RESULTS: Participants were mostly young males. The seroconversion rate was above 98% among those seronegative before immunization. Compared to placebo, the excess risk of any local adverse events ranged from 0.9% to 2.5%, whereas for any systemic adverse events it ranged from 3.5% to 7.4% across vaccine groups. The excess risk of events leading to search for medical care or to interruption of work activities ranged from 2% to 4.5%. Viremia was detected in 3%-6% of vaccinees up to 10 days after vaccination. Variations in liver enzyme levels after vaccination were similar in placebo and vaccine recipients. CONCLUSIONS: The frequency of adverse events post-immunization against YF, accounting for the background occurrence of nonspecific signs and symptoms, was shown for the first time to be similar for vaccines from 17D and 17DD substrains. The data also provided evidence against viscerotropism of vaccine virus.

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.

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.

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.

Gold electrode modified by self-assembled monolayers of thiols to determine DNA sequences hybridization

The process of immobilization of biological molecules is one of the most important steps in the construction of a biosensor. In the case of DNA, the way it exposes its bases can result in electrochemical signals to acceptable levels. The use of self-assembled monolayer that allows a connection to the gold thiol group and DNA binding to an aldehydic ligand resulted in the possibility of determining DNA hybridization. Immobilized single strand of DNA (ssDNA) from calf thymus pre-formed from alkanethiol film was formed by incubating a solution of 2-aminoethanothiol (Cys) followed by glutaraldehyde (Glu). Cyclic voltammetry (CV) was used to characterize the self-assembled monolayer on the gold electrode and, also, to study the immobilization of ssDNA probe and hybridization with the complementary sequence (target ssDNA). The ssDNA probe presents a well-defined oxidation peak at +0.158 V. When the hybridization occurs, this peak disappears which confirms the efficacy of the annealing and the DNA double helix performing without the presence of electroactive indicators. The use of SAM resulted in a stable immobilization of the ssDNA probe, enabling the hybridization detection without labels. This study represents a promising approach for molecular biosensor with sensible and reproducible results.