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.

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.

Fractional Analysis of the DNA Information

Proceedings of the 12th Conference on 'Dynamical Systems -Theory and Applications'

Effects of Chlorophenoxy Herbicides and Their Main Transformation Products on DNA Damage and Acetylcholinesterase Activity

Persistent pesticide transformation products (TPs) are increasingly being detected among different environmental compartments, including groundwater and surface water. However, there is no sufficient experimental data on their toxicological potential to assess the risk associated with TPs, even if their occurrence is known. In this study, the interaction of chlorophenoxy herbicides (MCPA, mecoprop, 2,4-D and dichlorprop) and their main transformation products with calf thymus DNA by UV-visible absorption spectroscopy has been assessed. Additionally, the toxicity of the chlorophenoxy herbicides and TPs was also assessed evaluating the inhibition of acetylcholinesterase activity. On the basis of the results found, it seems that AChE is not the main target of chlorophenoxy herbicides and their TPs. However, the results found showed that the transformation products displayed a higher inhibitory activity when compared with the parent herbicides. The results obtained in the DNA interaction studies showed, in general, a slight effect on the stability of the double helix. However, the data found for 4-chloro-2-methyl-6-nitrophenol suggest that this transformation product can interact with DNA through a noncovalent mode.