Computational Aspects of Protein Functionality

The purpose of this short article is to examine certain aspects of protein functionality with relation to some key organizing ideas. This is important from a computational viewpoint in order to take account of modelling both biological systems and knowledge of these systems. We look at some of the lexical dimensions of the function and how certain constructs can be related to underlying ideas. The pervasive computational metaphor is then discussed in relation to protein multifunctionality, and the specific case of von Willebrand factor as a ‘smart’ multifunctional protein is briefly considered. Some diagrammatic techniques are then introduced to better articulate protein function

Individual-Based Modelling of Bacterial Ecologies and Evolution

This paper presents two approaches to the individual-based modelling of bacterial ecologies and evolution using computational tools. The first approach is a fine-grained model that is based on networks of interactivity between computational objects representing genes and proteins. The second approach is a coarser-grained, agent-based model, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of these computational models is discussed, and some results from simulation experiments are presented. Finally, the potential applications of the proposed models to the solution of real-world computational problems, and their use in improving our understanding of the mechanisms of evolution, are briefly outlined

Breeding Ecology and Behavior of the Hawaiian Hawk

We studied the ecology of the endangered Hawaiian Hawk (Buteo solitarius) on the island of Hawaii for three breeding seasons. Their breeding strategy is a prime example of a K-selected species characteristic of many birds in tropical environments: clutch size was one and brood-rearing was among the longest reported for any diurnal raptor. Twenty-eight nests were found in a variety of native and exotic habitats. Incubation lasted 38 days, nestlings fledged after 59-63 days, and parents cared for fledglings for an average of 30.2 weeks, which was 2.5 to 10 times longer than similar-size temperate zone raptors. Males assisted females with incubation, but only females brooded young. Radio-tagged juveniles remained within 0.63 km of their nests for the first two months after fledging, after which dispersal distances expanded gradually. Avian (45%) and mammalian (54%) prey dominated the diet of nestlings. There was no evidence that avian malaria, introduced predators, or environmental contaminants were affecting their population. Based upon estimates of population size, the availability of suitable nesting habitat, and reproductive success, we suggest the species be considered for downlisting from endangered to threatened status

Site Fidelity, Philopatry, and Survival of Promiscuous Saltmarsh Sharp-Tailed Sparrows in Rhode Island

We investigated site fidelity and apparent survival in a promiscuous population of Saltmarsh Sharp-tailed Sparrows (Ammodramus caudacutus) in southern Rhode Island. Based on capture–recapture histories of 446 color-banded sparrows studied from 1993 to 1998 at our primary study site, Galilee, we observed significant variation in apparent survival rates among years, but not between sexes. Return rates of adult males (37.6%) and females (35.6%) were not significantly different during any year. Juveniles exhibited high return rates, ranging from 0 to 44%, with males (61% of returns) more likely to return than females (35%). In addition, we monitored movements of 404 color-banded sparrows at nine satellite marshes in 1997 and 1998, which supported our findings at Galilee and documented intermarsh movements by 10% of all banded birds. Lack of gender-bias in adult dispersal and strong natal philopatry of sparrows in Rhode Island occurs regularly among passerines possessing a variety of mating systems. Despite emancipation from parental and resource defense duties, adult male Saltmarsh Sharp-tailed Sparrows exhibited apparent survival rates similar to adult females. Availability of high-quality breeding habitat, which is patchy and saturated, may be the most important factor limiting dispersal for Saltmarsh Sharp-tailed Sparrows in Rhode Island

IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress

IRE1β is an ER stress sensor uniquely expressed in epithelial cells lining mucosal surfaces. Here, we show that intestinal epithelial cells expressing IRE1β have an attenuated unfolded protein response to ER stress. When modeled in HEK293 cells and with purified protein, IRE1β diminishes expression and inhibits signaling by the closely related stress sensor IRE1α. IRE1β can assemble with and inhibit IRE1α to suppress stress-induced XBP1 splicing, a key mediator of the unfolded protein response. In comparison to IRE1α, IRE1β has relatively weak XBP1 splicing activity, largely explained by a nonconserved amino acid in the kinase domain active site that impairs its phosphorylation and restricts oligomerization. This enables IRE1β to act as a dominant-negative suppressor of IRE1α and affect how barrier epithelial cells manage the response to stress at the host–environment interface

Development of a Grazing Land Management Education Program for Northern Australia’s Grasslands and Grassy Woodlands

Recognition of the potential to enhance grazing land management to meet the goal of sustainable beef production has been increasing over the past decade. Recognition of the relationship between poor land management and negative off-site environmental impacts, such as soil erosion and a decline in the condition of rivers and adjacent near shore coastal areas from sediment transport, has increased also. This concern has matured somewhat to include the critical link between land condition and production, and the threat to sustainable carrying capacity that comes from declining land condition. Concurrently, interest has increased in optimising the use of pasture, e.g. through the development of infrastructure (watering points, fencing), through more pro-active management e.g. alternative grazing systems, spelling of pastures, and through pasture development. In fact, it can be argued that achieving production goals while improving and maintaining the health of the land has become the major on-property issue for northern Australian graziers

Undergraduate teaching in geriatric medicine: mapping the British Geriatrics Society undergraduate curriculum to Tomorrow's Doctors 2009

Introduction: in 2008, the British Geriatrics Society (BGS) developed the Recommended Undergraduate Curriculum in Geriatric Medicine. This was subsequently mapped to the second edition of Tomorrows' Doctors (TD2, 2003). Following the publication of the third edition of Tomorrow's Doctors in 2009 (TD3), the mapping exercise was repeated to verify the extent to which the updated General Medical Council recommendations supported teaching in ageing and geriatric medicine. Method: we analysed TD3 and identified 48 aspects of its general guidance that were relevant to the teaching of medicine for older people. We then mapped these to the 2009 BGS curriculum. Results: the BGS curriculum was supported in full by TD3. However, learning outcomes relating to the interpretation and conduct of research in TD3 had no corresponding outcomes in the BGS curriculum. Conclusion: the BGS curriculum for medical undergraduates continues to provide a specific and complete list of learning objectives, all of which could help to operationalise the general statements made in TD3 with relation to ageing and geriatric medicine. Learning outcomes in research in frail older patients have been added following this mapping exercise

Three-body dispersion-relation N/D equations for the coupled decay channels ppbar (J^{PC}=0^{-+}) --> pi^0 pi^0 pi^0, eta pi^0 pi^0, eta eta pi^0, K Kbar pi^0

During several years the data on different channels ppbar (J^{PC}=0^{-+}) --> 3 mesons presented by Crystal Barrel Collaboration were successfully analyzed by extracting the leading amplitude singularities - pole singularities - with the aim to obtain information about two-meson resonances. But these analyses do not take into account three-body final state interactions (FSI) in an explicitly correct way. This paper is devoted to the consideration of this problem.Comment: 16 pages, no figure