Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

The Effect of the Small Indian Mongoose (Urva auropunctatus), Island Quality and Habitat on the Distribution of Native and Endemic Birds on Small Islands within Fiji

This study investigated the effect of the presence of introduced mongoose, environmental quality and habitat on the distribution of native and endemic birds on 16 small islands within Fiji. In total, 9055 birds representing 45 species were observed within four key habitats (forest, villages, crop land and coastal vegetation) on the 16 islands, half of which had mongoose present. Previous studies attribute bird declines and extirpation anecdotally to the mongoose. The presence of mongoose, environmental quality and habitat type had a measurable influence on observed extant native and endemic bird communities. We conclude that three ground birds; Gallirallus phillipensis, Anas supericiliosa and Porphyrio porhyrio were negatively influenced by the presence of mongoose and that Ptilinopus perousii, Phigys solitarius, Chrysoenas victor, Ducula latrans, Clytorhyrchus vitiensis, Pachycephala pectoralis, Prospeia tabunesis, and Foulehaio carunculata were particularly dependent on good quality forest habitat. Conservation priorities in relation to protecting Fiji’s endemic birds from the effect of mongoose are discussed and preventative measures suggested

What a difference a bay makes: natural variation in dietary resources mediates growth in a recently settled herbivorous fish

Processes acting during the early stages of coral reef fish life cycles have a disproportionate influence on their adult abundance and community structure. Higher growth rates, for example, confer a major fitness advantage in larval and juvenile fishes, with larger fish undergoing significantly less mortality. The role of dietary resources in the size-structuring process has not been well validated, especially at the early post-settlement phase, where competition and predation are seen as preeminent drivers of juvenile fish assemblage structure. Here, we report on a size differential of 10–20% between recently settled Siganus spinus rabbitfish recruits from different bays around the Pacific island of Guam. This difference was maintained across multiple recruitment events within and between years. After confirming the validity of our observations through otolith increment analysis, subsequent investigation into the drivers of this variation revealed significant differences in the structure of algal assemblages between bays, congruent with the observed differences in size of the recently settled fish. Gut analyses showed a greater presence of algal types with higher levels of nitrogen and phosphorus in the stomachs of fish from Tanguisson, the bay with the largest observed recruits. To ensure this mechanism was one of causation and not correlation, we conducted a fully factorial experiment in which S. spinus recruits sampled from different bays were reared on all combinations of algal diets representative of the different bays. Recruits on the ‘Tanguisson’ diet grew faster than recruits on other diets, regardless of their origin. We propose that the greater availability of high-quality dietary resources at this location is likely conferring benefits that impact on the population-level dynamics of this species. The spatial and temporal extent of this process clearly implicates food as a limiting resource, capable of mediating fish population dynamics at multiple spatial scales and ontogenetic phases

Review of the life history characteristics, ecology and fisheries for deep-water tropical demersal fish in the Indo-Pacific region

© 2016, Her majesty the Queen in Right of Australia.Deep-water tropical fishes support locally significant commercial fisheries, high value recreational fisheries, and culturally and economically important artisanal and subsistence fisheries throughout the Indo-Pacific region. The main species captured by these fisheries are deep-water snappers (Lutjanidae), groupers (Epinephelidae), and emperors (Lethrinidae). Quantitative assessments of deep-water tropical fisheries have been limited by a lack of adequate biological and fisheries data. We review the biology and ecology of deep-water tropical fishes, discuss the implications for assessment and management of tropical deep-water fisheries, and provide perspectives on future research priorities. We found that biological and fisheries information is lacking for the majority of deep-water tropical fishes. Furthermore, many studies were constrained by low samples sizes and the use of methods that have not been validated or verified. Most species for which reliable information was available were reported to have extended longevities (>20 years), low rates of natural mortality (M < 0.15), and slow to modest growth rates (K = 0.12–0.25). These life history traits indicate a low production potential for many deep-water tropical fishes, and suggest that sustainable exploitation rates and potential yields may be low. There is a need for more representative and adequate studies of deep-water tropical fishes and for improved fisheries data collection and the use of consistent methods in addition to information sharing to facilitate the development of robust data-poor assessment techniques for these species