From biomedicine to natural history research: EST resources for ambystomatid salamanders

BACKGROUND: Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories. RESULTS: Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species. CONCLUSIONS: Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.Fundacao de Amparo e Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Coordenacao de Aperfeicofamento de Pessoal de Nivel Superior (CAPES)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq

A cross sectional evaluation of a total smoking ban at a large Australian university

Background: Total smoking bans have been found to contribute positively to the health of non-smokers by reducing exposure to second-hand smoke, and to enhance the likelihood of cessation among smokers. Methods: Two cross-sectional electronic surveys of staff and students at a large Australian university were conducted prior (n = 969) and 1 year post (n = 670) the implementation of a smoke free campus policy. Demographics, tobacco use, intention to quit, attitudes towards smoking and smoking restrictions and awareness of and attitudes towards the campus smoking policy were measured. Results: Exposure to second-hand smoke (SHS) reduced significantly (p &lt; 0.001) one year after policy implementation. Smoking prevalence was similar at both time periods (T1 9.3 %; T2 8.4 %) and over half of smokers indicated they were planning to quit smoking in the future (T1 65.5 vs T2 62.3 %). There was a significant increase in positive responses to the statement the campus should be totally smoke free including all outdoor areas at T2 compared to T1 (T1 60.8 vs T2 71.4 %; p &lt; 0.001), however respondents felt there should be places on campus for smokers to smoke (T1 53.6 vs T2 47 %; p &lt; 0.05). Conclusions: This study found a significant positive difference in exposure SHS after implementation of the total ban. Although prevalence of smoking in this study was low, the proportion of respondents who were contemplating smoking cessation suggests support for smokers would be beneficial. Continued awareness raising, education and enforcement is likely to enhance the long term outcomes of the total ban

The Global Research Neglect of Unassisted Smoking Cessation: Causes and Consequences

Simon Chapman and Ross MacKenzie review the evidence and argue that health promotion messages should emphasize that the most successful method used by most ex-smokers is unassisted cessation

Changing behaviour 'more or less'-do theories of behaviour inform strategies for implementation and de-implementation? A critical interpretive synthesis

BACKGROUND: Implementing evidence-based care requires healthcare practitioners to do less of some things (de-implementation) and more of others (implementation). Variations in effectiveness of behaviour change interventions may result from failure to consider a distinction between approaches by which behaviour increases and decreases in frequency. The distinction is not well represented in methods for designing interventions. This review aimed to identify whether there is a theoretical rationale to support this distinction. METHODS: Using Critical Interpretative Synthesis, this conceptual review included papers from a broad range of fields (biology, psychology, education, business) likely to report approaches for increasing or decreasing behaviour. Articles were identified from databases using search terms related to theory and behaviour change. Articles reporting changes in frequency of behaviour and explicit use of theory were included. Data extracted were direction of behaviour change, how theory was operationalised, and theory-based recommendations for behaviour change. Analyses of extracted data were conducted iteratively and involved inductive coding and critical exploration of ideas and purposive sampling of additional papers to explore theoretical concepts in greater detail. RESULTS: Critical analysis of 66 papers and their theoretical sources identified three key findings: (1) 9 of the 15 behavioural theories identified do not distinguish between implementation and de-implementation (5 theories were applied to only implementation or de-implementation, not both); (2) a common strategy for decreasing frequency was substituting one behaviour with another. No theoretical basis for this strategy was articulated, nor were methods proposed for selecting appropriate substitute behaviours; (3) Operant Learning Theory makes an explicit distinction between techniques for increasing and decreasing frequency. DISCUSSION: Behavioural theories provide little insight into the distinction between implementation and de-implementation. Operant Learning Theory identified different strategies for implementation and de-implementation, but these strategies may not be acceptable in health systems. Additionally, if behaviour substitution is an approach for de-implementation, further investigation may inform methods or rationale for selecting the substitute behaviour

We're in this Together: Sensation of the Host Cell Environment by Endosymbiotic Bacteria

Bacteria inhabit diverse environments, including the inside of eukaryotic cells. While a bacterial invader may initially act as a parasite or pathogen, a subsequent mutualistic relationship can emerge in which the endosymbiotic bacteria and their host share metabolites. While the environment of the host cell provides improved stability when compared to an extracellular environment, the endosymbiont population must still cope with changing conditions, including variable nutrient concentrations, the host cell cycle, host developmental programs, and host genetic variation. Furthermore, the eukaryotic host can deploy mechanisms actively preventing a bacterial return to a pathogenic state. Many endosymbionts are likely to use two-component systems (TCSs) to sense their surroundings, and expanded genomic studies of endosymbionts should reveal how TCSs may promote bacterial integration with a host cell. We suggest that studying TCS maintenance or loss may be informative about the evolutionary pathway taken toward endosymbiosis, or even toward endosymbiont-to-organelle conversion.Peer reviewe

Where Do Vapers Buy Their Vaping Supplies? Findings from the International Tobacco Control (ITC) 4 Country Smoking and Vaping Survey

Aim: This study examines where vapers purchase their vaping refills in countries having different regulations over such devices, Canada (CA), the United States (US), England (EN), and Australia (AU). Methods: Data were available from 1899 current adult daily and weekly vapers who participated in the 2016 (Wave 1) International Tobacco Control Four Country Smoking and Vaping. The outcome was purchase location of vaping supplies (online, vape shop, other). Adjusted odds ratios and 95% confidence intervals were reported for between country comparisons. Results: Overall, 41.4% of current vapers bought their vaping products from vape shops, 27.5% bought them online, and 31.1% from other retail locations. The vast majority of vapers (91.1%) reported using nicotine-containing e-liquids. In AU, vapers were more likely to buy online vs other locations compared to CA (OR = 6.4, 2.3⁻17.9), the US (OR = 4.1, 1.54⁻10.7), and EN (OR = 7.9, 2.9⁻21.8). In the US, they were more likely to buy from vape shops (OR = 3.3, 1.8⁻6.2) or online (OR = 1.9, 1.0⁻3.8) vs other retail locations when compared to those in EN. In CA, vapers were more likely to purchase at vape shops than at other retail locations when compared to vapers in EN (5.9, 3.2⁻10.9) and the US (1.87, 1.0⁻3.1). Conclusions: The regulatory environment and enforcement of such regulations appear to influence the location where vapers buy their vaping products. In AU, banning the retail sale of nicotine vaping products has led vapers to rely mainly on online purchasing sources, whereas the lack of enforcement of the same regulation in CA has allowed specialty vape shops to flourish