Motivation: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find the coordinates for their position in a continuous space. This distribution of positions has two properties: it is unique, and the source sequence can be recovered from the coordinates such that distance between positions measures similarity between the corresponding sequences. The possibility of using the latter property to identify succession schemes have been entirely overlooked in previous studies which raises the possibility that CGR may be upgraded from a mere representation technique to a sequence modeling tool. Results: The distribution of positions in the CGR plane were shown to be a generalization of Markov chain probability tables that accommodates non-integer orders. Therefore, Markov models are particular cases of CGR models rather than the reverse, as currently accepted. In addition, the CGR generalization has both practical (computational efficiency) and fundamental (scale independence) advantages. These results are illustrated by using Escherichia coli K-12 as a test data-set, in particular, the genes thrA , thrB and thrC of the threonine operon. Availability: A web page interface has been created where analyses of arbitrary sequences by CGR can be performed on-line (http://www.itqb.unl.pt:1111/biomat/resources/resources.htm). The test data-set used in this report is also included. Contact: almeidaj@musc.edu; mfletcher@biol.sc.edu

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. The data suggest a step-wise shutdown occurs in organismal death that is manifested by the apparent increase of certain transcripts with various abundance maxima and durations.

Vertical elevation relative to mean sea level is a critical variable for the productivity and stability of salt marshes. This research classified a high spatial resolution Airborne Data Acquisition and Registration (ADAR) digital camera image of a salt marsh landscape at North Inlet, South Carolina, USA using an artificial neural network. The remote sensing‐derived thematic map was cross‐referenced with Light Detection and Ranging (LIDAR) elevation data to compute the frequency distribution of marsh elevation relative to tidal elevations. At North Inlet, the median elevation of the salt marsh dominated by Spartina alterniflora was 0.349 m relative to the North American Vertical Datum 1988 (NAVD88), while the mean high water level was 0.618 m (2001 to May, 2003) with a mean tidal range of 1.39 m. The distribution of elevations of Spartina habitat within its vertical range was normal, and 80% of the salt marsh was situated between a narrow range of 0.22 m and 0.481 m. Areas classified as Juncus marsh, dominated by Juncus roemerianus, had a broader, skewed distribution, with 80% of the distribution between 0.296 m and 0.981 m and a median elevation of 0.519 m. The Juncus marsh occurs within the intertidal region of brackish marshes and along the upper fringe of salt marshes. The relative elevation of the Spartina marsh at North Inlet is consistent with recent work that predicts a decrease in equilibrium elevation with an increasing rate of sea‐level rise and suggests that the marshes here have not kept up with an increase in the rate of sea‐level rise during the last two decades.

Hybridization of rRNAs to microarrays is a promising approach for prokaryotic and eukaryotic species identification. Typically, the amount of bound target is measured by fluorescent intensity and it is assumed that the signal intensity is directly related to the target concentration. Using thirteen different eukaryotic LSU rRNA target sequences and 7693 short perfect match oligonucleotide probes, we have assessed current approaches for predicting signal intensities by comparing Gibbs free energy (Δ G °) calculations to experimental results. Our evaluation revealed a poor statistical relationship between predicted and actual intensities. Although signal intensities for a given target varied up to 70-fold, none of the predictors were able to fully explain this variation. Also, no combination of different free energy terms, as assessed by principal component and neural network analyses, provided a reliable predictor of hybridization efficiency. We also examined the effects of single-base pair mismatch (MM) (all possible types and positions) on signal intensities of duplexes. We found that the MM effects differ from those that were predicted from solution-based hybridizations. These results recommend against the application of probe design software tools that use thermodynamic parameters to assess probe quality for species identification. Our results imply that the thermodynamic properties of oligonucleotide hybridization are by far not yet understood.