New computational approaches for analysis of cis-regulatory networks

The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.     

A review: taking the sterile out of sterility

Users of in-dwelling medical devices, prostheses and surgical dressings rely implicitly on their sterility. Rarely do consumers give any thought to what sterility really means. The general assumption is that manufacturers have adopted the most efficient and cost-effective methods of achieving sterility. Currently, terminal sterilization processes appropriate for the manufacture of medical devices are those that are deemed to give less than one chance in a million of a single, finished product item containing a viable organism. Such a definition of sterility is embodied in the European standard EN556 as a Sterility Assurance Level of 10(-6), based on the properties of heat-resistant endospores. However, is this level of sterility assurance appropriate for all categories of medical device? Moreover, do all medical devices which are labelled as sterile require the same level of treatment? This paper will demonstrate that in some instances, the high standards set for sterilization processing are unreasonable, not cost-effective and exclude new sterilization technologies from being accepted by the regulatory authorities.     

Morphological diversity: taking the spine out of three-spine stickleback

A gene already known to play a crucial developmental role in chick and mouse embryos has been fingered as a candidate for naturally occurring variation in three-spine stickleback anatomy.     

Predicting rules on organization of cis-regulatory elements, taking the order of elements into account

MOTIVATION: In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements. RESULTS: We propose a method for detecting rules, by which the order of elements is restricted. The order restriction is expressed as element patterns. We extract all the element patterns that occur in promoter regions of at least the specified number of genes. Then, we find significant patterns based on the expression similarity of genes with promoter regions containing each of the extracted patterns. When we applied our method to Saccharomyces cerevisiae, we detected significant patterns overlooked by previous methods, thus demonstrating the utility of our method for analyses of eukaryotic gene regulation. We also suggest that several types of element organization exist: (i) those in which only the order of elements is important, (ii) order and distance both are important and (iii) only the combination of elements is important. AVAILABILITY: The program for extracting element patterns is available upon request.     

Canaries in the coal mine: a cross-species analysis of the plurality of obesity epidemics

A dramatic rise in obesity has occurred among humans within the last several decades. Little is known about whether similar increases in obesity have occurred in animals inhabiting human-influenced environments. We examined samples collectively consisting of over 20 000 animals from 24 populations (12 divided separately into males and females) of animals representing eight species living with or around humans in industrialized societies. In all populations, the estimated coefficient for the trend of body weight over time was positive (i.e. increasing). The probability of all trends being in the same direction by chance is 1.2 × 10(-7). Surprisingly, we find that over the past several decades, average mid-life body weights have risen among primates and rodents living in research colonies, as well as among feral rodents and domestic dogs and cats. The consistency of these findings among animals living in varying environments, suggests the intriguing possibility that the aetiology of increasing body weight may involve several as-of-yet unidentified and/or poorly understood factors (e.g. viral pathogens, epigenetic factors). This finding may eventually enhance the discovery and fuller elucidation of other factors that have contributed to the recent rise in obesity rates.     

ZooDDD: a cross-species database for digital differential display analysis

In this article, we combined EST information from the UniGene database and orthologous relationships from the Ensembl database to construct a ZooDDD database. The primary function of ZooDDD is to mine evolutionary conserved, highly expressed, tissue-specific orthologues in model animals. The candidate genes of interest derived from the ZooDDD database will provide biologists with a good step for comparing the expression, functions and evolution of animal genomes. AVAILABILITY: http://bio301.iis.sinica.edu.tw/~ZooDDDNew/main.php.     

On the nature of the species problem and the four meanings of 'species'

Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term 'species' as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem.     

Divergence across diet,time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.