Statistical, Computational and Visualization Methodologies to Unveil Gene Primary Structure Features

Objectives: Gene sequence features such as codon bias, codon context, and codon expansion (e.g. tri-nucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis.

Methods: Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do not provide easy computational and statistical tools to carry out detailed gene primary structure analysis on a genomic scale. We propose the usage of several statistical methods – contingency table analysis, residual analysis, multivariate analysis (cluster analysis) – to analyze the codon bias under various aspects (degree of association, contexts and clustering).

Results: The developed solution is a software application that provides a user-guided analysis of codon sequences considering several contexts and codon usage on a genomic scale. The utilization of this tool in our molecular biology laboratory is focused on particular genomes, especially those from Saccharomyces cerevisiae, Candida albicansand Escherichia coli. In order to illustrate the applicability and output layouts of the software these species are herein used as examples.

Conclusions: The statistical tools incorporated in the system are allowing to obtain global views of important sequence features. It is expected that the results obtained will permit identification of general rules that govern codon context and codon usage in any genome. Additionally, identification of genes containing expanded codons that arise as a consequence of erroneous DNA replication events will permit uncovering new genes associated with human disease.

Statistical, computational and visualization methodologies to unveil gene primary structure features

OBJECTIVES

Gene sequence features such as codon bias, codon context, and codon expansion (e.g. trinucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis.

METHODS

Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do not provide easy computational and statistical tools to carry out detailed gene primary structure analysis on a genomic scale. We propose the usage of several statistical methods--contingency table analysis, residual analysis, multivariate analysis (cluster analysis)--to analyze the codon bias under various aspects (degree of association, contexts and clustering).

RESULTS

The developed solution is a software application that provides a user-guided analysis of codon sequences considering several contexts and codon usage on a genomic scale. The utilization of this tool in our molecular biology laboratory is focused on particular genomes, especially those from Saccharomyces cerevisiae, Candida albicans and Escherichia coli. In order to illustrate the applicability and output layouts of the software these species are herein used as examples.

CONCLUSIONS

The statistical tools incorporated in the system are allowing to obtain global views of important sequence features. It is expected that the results obtained will permit identification of general rules that govern codon context and codon usage in any genome. Additionally, identification of genes containing expanded codons that arise as a consequence of erroneous DNA replication events will permit uncovering new genes associated with human disease.

[Necrotizing fasciitis after varicella]

Necrotizing fasciitis is a rare and severe infection characterised by extremely rapid progressive involvement of the superficial fascias and deep dermal layers of the skin, with resultant vasculitis and necrosis. The authors present three clinical cases of necrotizing fasciitis; all three patients previously had varicella rash, rapid progressive spreading erythema with severe pain and toxic shock syndrome. Two patients had positive cultures of b-haemolytic streptococcus. Early stage differential diagnosis with celulitis, aggressive antibiotic treatment and pediatric intensive care support are essential. However, the main therapy is early extensive surgical approach involving all indurate areas, down to and including the muscle fascia.

The action of Cd, Cu, Cr, Zn, and Pb on fluid composition of Anodonta cygnea (L.): organic components

The heavy metals, Cd, Cu, Cr, Zn, and Pb, were used to incubate healthy specimens of the freshwater mussel species, Anodonta cygnea. Afterwards, their biological fluids, either haemolymph or extrapallial fluid were analyzed for the presence of several organic constituents, known to be important for biomineralization, such as proteins, glycosaminoglycans (GAGs) and glucosamine. Proteins were subjected to further study, namely through the total amino acid determination after acid hydrolysis. The most disturbing pollutants tested seem to be Pb, Zn, and Cr, which caused highly decreased overall compositions, namely with respect to protein, and glucosamine, in comparison to the control group. This suggests that this group contributes to a decrease of the metabolic activity, and thus mineralization, in the exposed animals.

Trance surgery in Brazil

This report presents the results of fieldwork in Brazil on healer-mediums who perform crude forms of surgery, often employing sharp instruments. We found that these healer-mediums were in a hyperaroused brain state while they were engaged in behaviors commonly described in the anthropology literature as "possession trance"; therefore, this practice is termed "trance surgery" in this report. The research was conducted at widely scattered sites throughout Brazil. We observed several thousand patients being treated by 9 trance surgeons and videotaped several hundred of these cases. In addition to background information and our own observational material, this paper includes 2 medical case reports, physiological data gathered from healers and patients, and results of a pathologist's examination of a surgically excised tumor. Topographic brain mapping revealed increased brain activity (36-44 Hz) when healer-mediums were engaged in trance behaviors, compared to resting baseline conditions at midline scalp locations (Cz, P < .009 and Pz, P < .004; both matched t tests). These results suggest the presence of a hyperaroused brain state associated with the trance behaviors of the healers. We believe that such a state is required for this unusual practice, but other factors may also be involved. In contrast, a small sample of patients monitored during possession trance surgical procedures revealed no high-frequency brain activity; instead, there were indications of cortical quieting, suggesting relaxation, despite the absence of anesthesia. Pathohistological examination of a tumor excised from a patient in our presence revealed a human fibroadenoma. We conclude that these practices are usually benign and that pain is often absent, despite the lack of sterile procedures and anesthesia. Although during the period of our investigation we were informed anecdotally of 3 cases involving serious complications or death, we personally observed no cases of shock, hemorrhage, or death. The cases presented in this paper, as well as others we have followed, suggest that serious illnesses, not likely to improve without treatment, may do so after trance surgery procedures are performed. If the major benefit of trance surgery is to initiate self-healing processes, it would have to do so in powerful ways, which possibly can be elucidated with positron emission tomography and functional magnetic resonance imaging scans. Positive findings would be helpful in understanding large-scale healing effects and may lead to new treatment protocols.

Organic compounds in the extrapalial fluid and haemolymph of Anodonta cygnea (L.) with emphasis on the seasonal biomineralization process

Bivalve mollusks, such as the freshwater mussel Anodonta cygnea, show seasonal changes in calcification. This cycle of calcification must either be a cause or a consequence for seasonal fluctuations in the organic composition of the animal's fluids, haemolymph and extrapallial fluid, the liquid media for biomineralization. We monitored the fluids of A. cygnea, throughout a 1-year cycle, for the presence of organic constituents, known to be important for biomineralization, such as proteins, glycosaminoglycans (GAGs) and hexosamines. Proteins were subjected to further study, namely through the total amino acid determination and fraction separation by agarose gel electrophoresis. GAG levels were fairly constant throughout the year, with a maximum concentration in July and a minimum in January, a feature also detected for glucosamine, although with higher fluctuations. Proteins showed highly increased concentrations during June and July, both in total amounts and individual fractions. All fractions showed similar trends throughout the year, with lowest general levels in October, the starting month of a period when some fractions were not detectable at all. All fractions ended this low period in May, when a sometimes-important increase could be detected. As to the total amino acid composition of the fluids, the general trend followed that of proteins, except for ornithine (Orn), a non-proteic amino acid. The overall fluctuations detected in the biological fluids of A. cygnea suggest that the main variation related to the calcification cycle must be quantitative, since no different compounds appear in specific periods, to achieve also specific results.