Comparison of time series and mechanistic models of vector-borne diseases.

Vector-borne disease models are widely used to understand the dynamics involved in virus transmission. The simplest version of the mechanistic SEIR-SEI model is the most widely used representation of the dynamics involved in vector-borne diseases. Modifications to the basic model can improve the complex dynamics' acuracy. This work evaluates the capability of different models to represent the dynamics involved in dengue virus transmission. The models include a vector life stage representation, a re-susceptibility factor, and environmental variables in a mechanistic form. Furthermore, Autoregressive Integrated Moving Average methodologies (ARIMA method) were also used for comparison. The inclusion of environmental variables and vector life cycle improves the model's accuracy for mechanistic models, but the modification's complexity can restrict its applicability. Data-driven techniques were shown to be less accurate than all the mechanistic-based models (based on all criteria adopted).

Multi-cluster and environmental dependant vector born disease models.

Vector-born disease models are extensively used for surveillance and control processes. The most simple and generally use model (SEIR-SEI model) cannot explain a variety of phenomena involved in these diseases spread and development. In order to obtain a wider insight of the vector-born disease models (and the dynamics involved in them), this work focuses into analyse the classical model, a modified versions of it, and 8 their parameters. The modified version includes host mobility, 9 environmental, re-susceptibility, and mosquito life cycle considerations. As results it is observed that there are a limiting number of parameters that play the most important roles in the dynamics (those related to mortality rates, recovery rate from infectious, and pathogen transmission probabilities). Therefore, parameters determination should focus primarily into estimate these values. Stronger effects of the environmental variables are observed and expected by using different parameters and/or the use of multiple environmental variable at the same time.

CodonLogo: a sequence logo-based viewer for codon patterns.

MOTIVATION: Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns. RESULTS: We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos. AVAILABILITY: The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.

Codon size reduction as the origin of the triplet genetic code.

The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon-anticodon interactions.