Testing the effectiveness of two natural selection simulations in the context of a large‑enrollment undergraduate laboratory class

Background: Simulations can be an active and engaging way for students to learn about natural selection, and many have been developed, including both physical and virtual simulations. In this study we assessed the student experience of, and learning from, two natural selection simulations, one physical and one virtual, in a large enrollment introductory biology lab course. We assigned students to treatments (the physical or virtual simulation activity) by section and assessed their understanding of natural selection using a multiple-choice pre-/post-test and short-answer responses on a post-lab assignment. We assessed student experience of the activities through structured observations and an affective survey. Results: Students in both treatments showed increased understanding of natural selection after completing the simulation activity, but there were no differences between treatments in learning gains on the pre-/post-test, or in the prevalence of concepts and misconceptions in written answers. On a survey of self-reported enjoyment they rated the physical activity significantly higher than the virtual activity. In classroom observations of student behavior, we found significant differences in the distribution of behaviors between treatments, including a higher frequency of off task behavior during the physical activity. Conclusions: Our results suggest that both simulations are valuable active learning tools to aid students’ understanding of natural selection, so decisions about which simulation to use in a given class, and how to best implement it, can be motivated by contextual factors

Iterative Design of a Simulation-Based Module for Teaching Evolution by Natural Selection

Background: This research builds on a previous study that looked at the effectiveness of a simulation-based module for teaching students about the process of evolution by natural selection. While the previous study showed that the module was successful in teaching how natural selection works, the research uncovered some weaknesses in the design. In this paper, we used design-based research to investigate how design changes to the module affected not only students’ understanding of the concepts but also their usage of misconceptions in the assessments. We present results from two studies. In study 1, we looked at gains in understanding on a pre and post-assessment for students who used the revised version of the module. We also examined misconception uses in their answer selections. In study 2, we compared the performance on a summative assessment between students who used the revised version and students who used the original version of the module. We also looked at misconception uses in their answer selections. Results: In study 1, we saw a significant improvement in the pre-post assessment for students who used the revised version. In study 2, we did not find a significant difference on the overall performance outcome between students who used the revised and those that used the original version of the module. In both studies, however, we saw a lower use of misconceptions after students used the revised module. In particular, we saw less use of the adaptive mutation misconception, the belief that mutations are adaptive responses to the environment and are biased towards advantageous mutations. This is promising because in the previous study there was no evidence of decreased use of this misconception. Conclusions: Students showed learning gains on all targeted key concepts, and reduced expression of all targeted misconceptions, which was not found previously for students using the older workbook version of the module. In particular, the revised version appears to help students overcome the adaptive mutation misconception. This article demonstrates how design-based research can contribute to the ongoing improvement of evidence-based instruction in undergraduate biology classrooms

Using a realist approach to evaluate smoking cessation interventions targeting pregnant women and young people

Background This paper describes a study protocol designed to evaluate a programme of smoking cessation interventions targeting pregnant women and young people living in urban and rural locations in Northeast Scotland. The study design was developed on so-called 'realist' evaluation principles, which are concerned with the implementation of interventions as well as their outcomes. Methods/design A two-phased study was designed based on the Theory of Change (TOC) using mixed methods to assess both process and outcome factors. The study was designed with input from the relevant stakeholders. The mixed-methods approach consists of semi-structured interviews with planners, service providers, service users and non-users. These qualitative interviews will be analysed using a thematic framework approach. The quantitative element of the study will include the analysis of routinely collected data and specific project monitoring data, such as data on service engagement, service use, quit rates and changes in smoking status. Discussion The process of involving key stakeholders was conducted using logic modelling and TOC tools. Engaging stakeholders, including those responsible for funding, developing and delivering, and those intended to benefit from interventions aimed at them, in their evaluation design, are considered by many to increase the validity and rigour of the subsequent evidence generated. This study is intended to determine not only the components and processes, but also the possible effectiveness of this set of health interventions, and contribute to the evidence base about smoking cessation interventions aimed at priority groups in Scotland. It is also anticipated that this study will contribute to the ongoing debate about the role and challenges of 'realist' evaluation approaches in general, and the utility of logic modelling and TOC approaches in particular, for evaluation of complex health interventions

Evaluating implementation of a fire-prevention injury prevention briefing in children's centres: cluster randomised controlled trial

Background: Many developed countries have high mortality rates for fire-related deaths in children aged 0–14 years with steep social gradients. Evidence-based interventions to promote fire safety practices exist, but the impact of implementing a range of these interventions in children’s services has not been assessed. We developed an Injury Prevention Briefing (IPB), which brought together evidence about effective fire safety interventions and good practice in delivering interventions; plus training and facilitation to support its use and evaluated its implementation. Methods: We conducted a cluster randomised controlled trial, with integrated qualitative and cost-effectiveness nested studies, across four study sites in England involving children’s centres in disadvantaged areas; participants were staff and families attending those centres. Centres were stratified by study site and randomised within strata to one of three arms: IPB plus facilitation (IPB+), IPB only, usual care. IPB+ centres received initial training and facilitation at months 1, 3, and 8. Baseline data from children’s centres were collected between August 2011 and January 2012 and follow-up data were collected between June 2012 and June 2013. Parent baseline data were collected between January 2012 and May 2012 and follow-up data between May 2013 and September 2013. Data comprised baseline and 12 month parent- and staff-completed questionnaires, facilitation contact data, activity logs and staff interviews. The primary outcome was whether families had a plan for escaping from a house fire. Treatment arms were compared using multilevel models to account for clustering by children’s centre. Results: 1112 parents at 36 children’s centres participated. There was no significant effect of the intervention on families’ possession of plans for escaping from a house fire (adjusted odds ratio (AOR) IPB only vs. usual care: 0.93, 95%CI 0.58, 1.49; AOR IPB+ vs. usual care 1.41, 95%CI 0.91, 2.20). However, significantly more families in the intervention arms reported more behaviours for escaping from house fires (AOR IPB only vs. usual care: 2.56, 95%CI 01.38, 4.76; AOR IPB+ vs. usual care 1.78, 95%CI 1.01, 3.15). Conclusion: Our study demonstrated that children’s centres can deliver an injury prevention intervention to families in disadvantaged communities and achieve changes in home safety behaviours

Cytochrome c4 is required for siderophore expression by Legionella pneumophila, whereas cytochromes c1 and c5 promote intracellular infection

A panel of cytochrome c maturation (ccm) mutants of Legionella pneumophila displayed a loss of siderophore (legiobactin) expression, as measured by both the chrome azurol S assay and a Legionella-specific bioassay. These data, coupled with the finding that ccm transcripts are expressed by wild-type bacteria grown in deferrated medium, indicate that the Ccm system promotes siderophore expression by L. pneumophila. To determine the basis of this newfound role for Ccm, we constructed and tested a set of mutants specifically lacking individual c-type cytochromes. Whereas ubiquinol-cytochrome c reductase (petC) mutants specifically lacking cytochrome c1 and cycB mutants lacking cytochrome c5 had normal siderophore expression, cyc4 mutants defective for cytochrome c4 completely lacked legiobactin. These data, along with the expression pattern of cyc4 mRNA, indicate that cytochrome c4 in particular promotes siderophore expression. In intracellular infection assays, petC mutants and cycB mutants, but not cyc4 mutants, had a reduced ability to infect both amoebae and macrophage hosts. Like ccm mutants, the cycB mutants were completely unable to grow in amoebae, highlighting a major role for cytochrome c5 in intracellular infection. To our knowledge, these data represent both the first direct documentation of the importance of a c-type cytochrome in expression of a biologically active siderophore and the first insight into the relative importance of c-type cytochromes in intracellular infection events

The Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips

This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship. Both mammalian and insect hosts provide partial size reduction, chemical treatments (low or high pH environments), and complex enzymatic ‘secretomes’ that improve microbial access to cell wall polymers. We hypothesized that in order to efficiently degrade coarse untreated biomass, a spontaneously assembled free-living community must both employ alternative strategies, such as enzymatic lignin depolymerization, for accessing hemicellulose and cellulose and have a much broader metabolic potential than host-associated communities. This would suggest that such a community would make a valuable resource for finding new catalytic functions involved in biomass decomposition and gaining new insight into the poorly understood process of anaerobic lignin depolymerization. Therefore, in addition to determining the major players in this community, our work specifically aimed at identifying functions potentially involved in the depolymerization of cellulose, hemicelluloses, and lignin, and to assign specific roles to the prevalent community members in the collaborative process of biomass decomposition. A bacterium similar to Magnetospirillum was identified among the dominant community members, which could play a key role in the anaerobic breakdown of aromatic compounds. We suggest that these compounds are released from the lignin fraction in poplar hardwood during the decay process, which would point to lignin-modification or depolymerization under anaerobic conditions

Impacts of 21st century climate change on global air pollution-related premature mortality

Climate change modulates surface concentrations of fine particulate matter (PM2.5) and ozone (O-3), indirectly affecting premature mortality attributed to air pollution. We estimate the change in global premature mortality and years of life lost (YLL) associated with changes in surface O-3 and PM2.5 over the 21st century as a result of climate change. We use a global coupled chemistry-climate model to simulate current and future climate and the effect of changing climate on air quality. Epidemiological concentration-response relationships are applied to estimate resulting changes in premature mortality and YLL. The effect of climate change on air quality is isolated by holding emissions of air pollutants constant while allowing climate to evolve over the 21st century according to a moderate projection of greenhouse gas emissions (A1B scenario). Resulting changes in 21st century climate alone lead to an increase in simulated PM2.5 concentrations globally, and to higher (lower) O-3 concentrations over populated (remote) regions. Global annual premature mortality associated with chronic exposure to PM2.5 increases by approximately 100 thousand deaths (95 % confidence interval, CI, of 66-130 thousand) with corresponding YLL increasing by nearly 900 thousand (95 % CI, 576-1,128 thousand) years. The annual premature mortality due to respiratory disease associated with chronic O-3 exposure increases by +6,300 deaths (95 % CI, 1,600-10,400). This climate penalty indicates that stronger emission controls will be needed in the future to meet current air quality standards and to avoid higher health risks associated with climate change induced worsening of air quality over populated regions.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326944000011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Environmental SciencesMeteorology & Atmospheric SciencesSCI(E)EI17ARTICLE2239-25312

Considerations on the use of video playbacks as visual stimuli: The Lisbon workshop consensus

This paper is the consensus of a workshop that critically evaluated the utility and problems of video playbacks as stimuli in studies of visual behavior. We suggest that video playback is probably suitable for studying motion, shape, texture, size, and brightness. Studying color is problematic because video systems are specifically designed for humans. Any difference in color perception must lead to a different color sensation in most animals. Another potentially problematic limitation of video images is that they lack depth cues derived from stereopsis, accommodation, and motion parallax. Nonetheless, when used appropriately, video playback allows an unprecedented range of questions in visual communication to be addressed. It is important to note that most of the potential limitations of video playback are not unique to this technique but are relevant to all studies of visual signaling in animals

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio