A Web-Based Data Architecture for Problem-Solving Environments: Application of Distributed Authoring and Versioning to the Extensible Computational Chemistry Environment

Next-generation problem-solving environments (PSEs) promise significant advances over those now available. They will span scientific disciplines and incorporate collaboration capabilities. They will host feature-detection and other agents, allow data mining and pedigree tracking, and provide access from a wide range of devices. Fundamental changes in PSE architecture are required to realize these and other PSE goals. This paper focuses specifically on issues related to data management and recommends an approach based on open, metadata-driven repositories with loosely defined, dynamic schemas. Benefits of this approach are discussed, and the redesign of the Extensible Computational Chemistry Environment's (Ecce) data storage architecture to use such a repository is described, based on the distributed authoring and versioning (DAV) standard. The suitability of DAV for scientific data, the mapping of the Ecce schema to DAV, and promising initial results are presented.     

THE INCREASED POTENTIAL FOR SELECTION OF THE LAC OPERON OF ESCHERICHIA COLI

The fitness effects of six lac operons from natural isolates of Escherichia coli were determined in chemostats, in a test of the idea that selective differences among natural alleles are greater in novel conditions than in the prevailing environment, resulting in a greater genetic variance in fitness in novel conditions. Fitnesses were determined in the common milk sugar lactose, the natural substrate of the lac operon, and in three rare β-galactosides, lactulose, galactosyl-arabinose, and methyl-galactopyranoside, that are novel for E. coli. Significantly greater fitness differences were observed among the lac alleles in each of the novel β-galactosides than in lactose. An alternative explanation of the experimental findings is discussed. General evolutionary causes and consequences of selection potentials are discussed, and an outline of the work necessary to further elucidate the physiological basis of the observed potential for selection of the lac operon of E. coli is presented.     

The breeding of captive wild species by artificial methods

The growing interest in many zoos, wildlife parks and game ranches in the captive breeding of wild species has brought about much interest and research in developing and testing artificial methods of breeding. Much of this work has been concentrated in endangered species. The author outlines the relevance and utilization of such techniques and reviews successful attempts in this area and elaborates on future potential ones. A brief review is given of successful artificial methods of breeding domestic species and how this may be applied to non-domestic ones. Areas that are covered are semen collection, semen freezing, induction of estrus, artificial insemination, embryo transfer including interspecies transfer and embryo surgery. It is acknowledged that it is highly unlikely that an artificial program could save a species from extinction but such methods could greatly assist a comprehensive natural breeding program.     

A selection strategy to accommodate genotype-by-environment interaction for grain yield of wheat: managed-environments for selection among genotypes

Selection for grain yield among wheat lines is complicated by large line-by-environment (L × E) interactions in Queensland, Australia. Early generation selection is based on an evaluation of many lines in a few environments. The small sample of environments, together with the large L × E interaction, reduces the realised response to selection. Definition of a series of managed-environments which provides discrimination among lines, which is relevant to the target production-environments, and can be repeated over years, would facilitate early generation selection. Two series of managed-environments were conducted. Eighteen managed-environments were generated in Series-1 by manipulating nitrogen and water availability, together with the sowing date, at three locations. Nine managed-environments based on those from Series-1 were generated in Series-2. Line discrimination for grain yield in the managed-environments was compared to that in a series of 16 random production-environments. The genetic correlation between line discrimination in the managed-environments and that in the production-environments was influenced by the number and combination of managed-environments. Two managed-environment selection regimes, which gave a high genetic correlation in both Series-1 and 2, were identified. The first used three managed-environments, a high input (low water and nitrogen stress) environment with early sowing at three locations. The second used six managed-environments, a combination of a high input (low water and nitrogen stress) and medium input (water and nitrogen stress) with early sowing at three locations. The opportunities for using managed-environments to provide more reliable selection among lines in the Queensland wheat breeding programme and its potential limitations are discussed.     

Altered wing phenotypes of captive-bred migratory birds lower post-release fitness

Captive breeding and release to the wild is a globally important conservation tool. However, captivity can result in phenotypic changes that incur post-release fitness costs, especially if they affect strenuous or risky behaviours. Bird wing shape is critical for migration success and suboptimal phenotypes are strongly selected against. In this study, I demonstrate surprising plasticity of bird wing phenotypes in captivity for 4/16 studied species. In a model species, captive-born juveniles with wild wing phenotypes (a 1-mm longer distal primary flight feather) survived post-release at 2.7 times the rate of those with captive phenotypes (i.e. a shorter distal feather). Subtle phenotypic changes and their fitness impacts are more common than widely realised because they are easily overlooked. To improve captive breeding for conservation, practitioners must surveil phenotypic changes and find ways to mitigate them.     

Introducing an innovative semi‐captive environment for the Philippine tarsier (Tarsius syrichta)

In response to demands for research, captive breeding, and tourism, a semi‐captive environment was created for the Philippine tarsiers (Tarsius syrichta) in Corella, Bohol, Philippines. The 7600‐m² enclosure was continuous with the surrounding habitat, and utilized a unique predator control fence design and a lighting system to attract nocturnal insects. During 2 years of observation, the locations of over 500 tarsier sleeping sites were recorded. Tarsiers were found to prefer dense, low‐level vegetation in secondary forests, with perching sites averaging 2 m above the ground. Up to 10 tarsiers were observed within the enclosure at one time, which is a high density compared to densities based on home‐range estimates for wild tarsiers in the vicinity of the study site. In addition, the tarsiers were observed to be more social than previously reported. Zoo Biol 24:101–109, 2005. © 2005 Wiley‐Liss, Inc.     

Habitat selection within species ofDrosophila: a review of experimental findings

Summary Habitat selection whereby individuals within a population have different microhabitat preferences is possibly important for genetic diversity and stability. It has received a good deal of attention, especially forDrosophila populations. The literature is summarized and an attempt is made to reconcile what appear to be contradictory findings. Some generalizations are drawn: (1) individualDrosophila choose habitats in consistent and characteristic ways; (2) some microhabitat differences are more important to flies than others; (3) genetic factors influence habitat preferences; (4) experiential factors influence habitat preferences; (5) differences in processing ability moderate the influence of experience on habitat choice. It is argued that the traditional analysis of variance models are frequently not very helpful for visualizing the process, and a computational model is suggested instead.     

The ecology and taxonomy of halobacteria

Abstract Archaebacterial halophiles dominate naturally occurring brines as the concentration of salts approaches saturation. Although only 4 genera of these bacteria have been recognised ( Halobacterium, Halococcus, Natronobacterium, Natronococcus ), chemotaxonomic studies indicate that there are 4 or 5 additional distinct groups. Archaebacterial halophiles are extremely physiologically versatile, some examples being capable of an anaerobic fermentative mode of growth, others of growth linked to the reduction of sulphur compounds. Many strains contain retinal-based pigments producing light-mediated movements of ions across the cell membrane, that in some cases can be harnessed for energy generation. However, it is likely that under normal conditions, an aerobic, chemoorganotrophic mode of nutrition is adopted.