Microarray analysis identifies candidate genes for key roles in coral development.

BACKGROUND: Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development - when skeletogenesis is initiated, and symbionts are first acquired. RESULTS: Of 5081 unique peptide coding genes, 1084 were differentially expressed (P

An efficient Z-score algorithm for assessing sequence alignments.

We describe an alternative method for scoring of the pairwise alignment of two biological sequences. Designed to overcome the bias due to the composition of the alignment, it measures the distance (in standard deviations) between the given alignment and the mean value of all other alignments that can be obtained by a permutation of either sequence. We demonstrate that the standard deviation can be calculated efficiently. By concentrating upon the ungapped case, the mean and standard deviation can be calculated exactly and in two steps, the first being O(N) time, where N is the length of the sequence, the second in a fixed number of calculations, i.e., in O(1) time. We argue that this statistic is a more consistent measure than a similarity score based upon a standard scoring matrix. Even in the ungapped case, the statistic proves in many cases to be more accurate than the commonly used (FASTA) (Pearson and Lipman, 1988) gapped Z-score in which the sequence is matched against a random sample of the database. We demonstrate the use of the POZ-score as a secondary filter which screens out several well-known types of false positive, reducing the amount of manual screening to be done by the biologist.

A two-phase model for smoothly joining disparate growth phases in the macropodid Thylogale billardierii.

Generally, sigmoid curves are used to describe the growth of animals over their lifetime. However, because growth rates often differ over an animal's lifetime a single curve may not accurately capture the growth. Broken-stick models constrained to pass through a common point have been proposed to describe the different growth phases, but these are often unsatisfactory because essentially there are still two functions that describe the lifetime growth. To provide a single, converged model to age animals with disparate growth phases we developed a smoothly joining two-phase nonlinear function (SJ2P), tailored to provide a more accurate description of lifetime growth of the macropod, the Tasmanian pademelon Thylogale billardierii. The model consists of the Verhulst logistic function, which describes pouch-phase growth--joining smoothly to the Brody function, which describes post-pouch growth. Results from the model demonstrate that male pademelons grew faster and bigger than females. Our approach provides a practical means of ageing wild pademelons for life history studies but given the high variability of the data used to parametrise the second growth phase of the model, the accuracy of ageing of post-weaned animals is low: accuracy might be improved with collection of longitudinal growth data. This study provides a unique, first robust method that can be used to characterise growth over the lifespan of pademelons. The development of this method is relevant to collecting age-specific vital rates from commonly used wildlife management practices to provide crucial insights into the demographic behaviour of animal populations.

Discussion of "A Bayesian approach to DNA sequence segmentation".

This article discusses the results in Boys and Henderson (2004, Biometrics 60, 573-581) in which the authors propose a new approach to the classification of genomic DNA into a number of hidden Markov states with a variable order of dependency, potentially allowing for the high-throughput detection of structure within genomic DNA. This article is likely to be an important point of departure for further modeling of this type. We question whether the genome of the bacteriophage lambda is the most appropriate example with which to demonstrate the method's effectiveness, whether it can be expected that the method will carry over to genomes where there is only one direction of transcription and no operon structure, and suggest a graphical display that seems to offer insight into the results. It would be interesting to see an analysis that uses the codon alphabet.

Applying Lee-Carter under conditions of variable mortality decline.

The Lee-Carter method of mortality forecasting assumes an invariant age component and most applications have adopted a linear time component. The use of the method with Australian data is compromised by significant departures from linearity in the time component and changes over time in the age component. We modify the method to adjust the time component to reproduce the age distribution of deaths, rather than total deaths, and to determine the optimal fitting period in order to address non-linearity in the time component. In the Australian case the modification has the added advantage that the assumption of invariance is better met. For Australian data, the modifications result in higher forecast life expectancy than the original Lee-Carter method and official projections, and a 50 per cent reduction in forecast error. The model is also expanded to take account of age-time interactions by incorporating additional terms, but these are not readily incorporated into forecasts.

Potential effect of population and climate changes on global distribution of dengue fever: an empirical model.

BACKGROUND: Existing theoretical models of the potential effects of climate change on vector-borne diseases do not account for social factors such as population increase, or interactions between climate variables. Our aim was to investigate the potential effects of global climate change on human health, and in particular, on the transmission of vector-borne diseases. METHODS: We modelled the reported global distribution of dengue fever on the basis of vapour pressure, which is a measure of humidity. We assessed changes in the geographical limits of dengue fever transmission, and in the number of people at risk of dengue by incorporating future climate change and human population projections into our model. FINDINGS: We showed that the current geographical limits of dengue fever transmission can be modelled with 89% accuracy on the basis of long-term average vapour pressure. In 1990, almost 30% of the world population, 1.5 billion people, lived in regions where the estimated risk of dengue transmission was greater than 50%. With population and climate change projections for 2085, we estimate that about 5-6 billion people (50-60% of the projected global population) would be at risk of dengue transmission, compared with 3.5 billion people, or 35% of the population, if climate change did not happen. INTERPRETATION: We conclude that climate change is likely to increase the area of land with a climate suitable for dengue fever transmission, and that if no other contributing factors were to change, a large proportion of the human population would then be put at risk.