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

Autoinducer 2 signalling via the phosphotransferase FruA drives galactose utilization by Streptococcus pneumoniae resulting in hypervirulence

Communication between bacterial cells is crucial for the coordination of diverse cellular processes that facilitate environmental adaptation and, in the case of pathogenic species, virulence. This is achieved by the secretion and detection of small signaling molecules called autoinducers, a process termed quorum sensing. To date, the only signaling molecule recognized by both Gram-positive and Gramnegative bacteria is autoinducer 2 (AI-2), synthesized by the metabolic enzyme LuxS (S-ribosylhomocysteine lyase) as a by-product of the activated methyl cycle. Homologues of LuxS are ubiquitous in bacteria, suggesting a key role in interspecies, as well as intraspecies, communication. Gram-negative bacteria sense and respond to AI-2 via the Lsr ABC transporter system or by the LuxP/LuxQ phosphorelay system. However, homologues of these systems are absent from Gram-positive bacteria and the AI-2 receptor is unknown. Here we show that in the major human pathogen Streptococcus pneumoniae, sensing of exogenous AI-2 is dependent on FruA, a fructose-specific phosphoenolpyruvate-phosphotransferase system that is highly conserved in Gram-positive pathogens. Importantly, AI-2 signaling via FruA enables the bacterium to utilize galactose as a carbon source and upregulates the Leloir pathway, thereby leading to increased production of capsular polysaccharide and a hypervirulent phenotype

Distributing transmitters to maximize population-level representativeness in automated radio telemetry studies of animal movement

Telemetry is a powerful and indispensable tool for evaluating wildlife movement and distribution patterns, particularly in systems where opportunities for direct observation are limited. However, the effort and expense required to track individuals often results in small sample sizes, which can lead to biased results if the sample of tracked individuals does not fully capture spatial, temporal, and individual variability within the target population. To better understand the influence of sampling design on results of automated radio telemetry studies, we conducted a retrospective power analysis of very high frequency (VHF) radio telemetry data from the Motus Wildlife Tracking System for two species of birds along the United States Atlantic coast: a shorebird, the piping plover (Charadrius melodus), and a nearshore seabird, the common tern (Sterna hirundo). We found that ~ 100–150 tracked individuals were required to identify 90% of locations known to be used by the tracked population, with 40–50 additional individuals required to include 95% of used locations. For any number of individuals, the percentage of stations included in the sample was higher for common terns than for piping plovers when tags were deployed within a single site and year. Percentages of stations included increased for piping plovers when birds were tagged over multiple sites and, to a lesser extent, years, and increased with average length of the tracking period. The probability that any given receiver station used by the population would be included in a subsample increased with the number of birds tracked, station proximity to a migratory stopover or staging site, number of receiving antennas per station, and percentage of the tracked population present. Our results provide general guidance for the number and distribution of tagged birds required to obtain representative VHF telemetry data, while also highlighting the importance of accounting for station network configuration and species-specific differences in behavior when designing automated radio telemetry studies to address specific research questions. Our results have broad applications to remotely track movements of small-bodied migratory wildlife in inaccessible habitats, including predicting and monitoring effects of offshore wind energy development

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

Supportive Wind Conditions Influence Offshore Movements of Atlantic Coast Piping Plovers during Fall Migration

In advance of large-scale development of offshore wind energy facilities throughout the U.S. Atlantic Outer Continental Shelf (OCS), information on the migratory ecology and routes of federally threatened Atlantic Coast Piping Plovers (Charadrius melodus melodus) is needed to conduct risk assessments pursuant to the Endangered Species Act. We tagged adult Piping Plovers (n = 150) with digitally coded VHF transmitters at 2 breeding areas within the southern New England region of the U.S. Atlantic coast from 2015 to 2017. We tracked their migratory departure flights using a regional automated telemetry network (n = 30 stations) extending across a portion of the U.S. Atlantic Bight region, a section of the U.S. Atlantic coast, and adjacent waters of the Atlantic Ocean extending from Cape Cod, Massachusetts, to Cape Hatteras, North Carolina. Most adults departed within a 10-day window from July 19 to July 29, migrated nocturnally, and over 75% of individuals departed within 3 hr of local sunset on evenings with supportive winds. Piping Plovers migrated offshore directly across the mid-Atlantic Bight, from breeding areas in southern New England to stopover sites spanning from New York to North Carolina, USA, over 800 km away. During offshore migratory flights, Piping Plovers flew at estimated mean speeds of 42 km hr−1 and altitudes of 288 m (range of model uncertainty: 36–1,031 m). This study provides new information on the timing, weather conditions, routes, and altitudes of Piping Plovers during fall migration. This information can be used in estimations of collision risk that could potentially result from the construction of offshore wind turbines under consideration across large areas of the U.S. Atlantic OCS

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

How to increase earthquake and home fire preparedness: the fix-it intervention

Published, evaluated community intervention studies concerning natural hazard preparedness are rare. Most lack a rigorous methodology, thereby hampering the development of evidence-based interventions. This paper describes the rationale and methodology of a cross-cultural, longitudinal intervention study on earthquake and home fire preparedness, termed fix-it. The aim is to evaluate whether and how the intervention brings about behaviour change in the targeted communities in two coastal cities with high seismic risk: Seattle, USA and Izmir, Turkey. Participants are adult residents of these cities. The intervention group attends a 6-h workshop, which focuses on securing items in the household. The control group does not attend the workshop. All participants complete baseline and post-intervention, as well as 3- and 12-month follow-up assessments. The primary outcome measure is an observational measure of nine preparedness items for earthquake and fire in participants’ homes. This is evaluated alongside participants’ self-reports concerning their preparedness levels. Secondary outcomes are changes in levels of self-efficacy, perceived outcome, trust, corruption, empowerment, anxiety and social cohesion. Results from the first of the studies, conducted in Seattle in September 2015, indicate that while the fix-it intervention is effective, in the longer term, multi-hazard preparedness is increased by the mere act of going into people’s homes to observe their preparedness levels along with assessing self-reported preparedness and sociopsychological orientation towards natural hazards. This protocol and study aim to augment the empirical literature on natural hazard preparedness, informing national and international policy on delivery of evidence-based community interventions to promote multi-hazard preparedness in households

Genetic Diversity and Virulence Potential of Shiga Toxin-Producing Escherichia coli O113:H21 Strains Isolated from Clinical, Environmental, and Food Sources

Shiga toxin-producing Escherichia coli strains of serotype O113:H21 have caused severe human diseases, but they are unusual in that they do not produce adherence factors coded by the locus of enterocyte effacement. Here, a PCR microarray was used to characterize 65 O113:H21 strains isolated from the environment, food, and clinical infections from various countries. in comparison to the pathogenic strains that were implicated in hemolytic-uremic syndrome in Australia, there were no clear differences between the pathogens and the environmental strains with respect to the 41 genetic markers tested. Furthermore, all of the strains carried only Shiga toxin subtypes associated with human infections, suggesting that the environmental strains have the potential to cause disease. Most of the O113:H21 strains were closely related and belonged in the same clonal group (ST-223), but CRISPR analysis showed a great degree of genetic diversity among the O113:H21 strains.French Joint Ministerial Program of R&D against CBRNE RisksFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Food & Drug Adm, Div Microbiol, College Pk, MD 20740 USAFrench Agcy Food Environm & Occupat Hlth & Safety, Lab Food Safety, Maisons Alfort, FranceFood & Drug Adm, Div Mol Biol, Laurel, MD USAUniversidade Federal de São Paulo, Dept Microbiol Immunol & Parasitol, São Paulo, BrazilFed Inst Risk Assessment, Natl Reference Lab Escherichia coli, Berlin, GermanyInst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Serv Fisiopatogenia, Buenos Aires, DF, ArgentinaUniv Melbourne, Peter Doherty Inst Infect & Immun, Dept Microbiol & Immunol, Melbourne, Vic, AustraliaUniv Adelaide, Res Ctr Infect Dis, Sch Mol & Biomed Sci, Adelaide, SA, AustraliaUniversidade Federal de São Paulo, Dept Microbiol Immunol & Parasitol, São Paulo, BrazilFrench Joint Ministerial Program of R&D against CBRNE Risks: C17609-2Web of Scienc