Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

<p>Abstract</p> <p>Background</p> <p>The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20^thcentury. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease.</p> <p>Results</p> <p>Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through <it>in toto </it>transfer of an avian influenza virus.</p> <p>Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes.</p> <p>Conclusions</p> <p>Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.</p

Local governance in the new Police Scotland:Renegotiating power, recognition and responsiveness

A marked, but by no means universal, trend in Europe over the last decade or so has been the centralization or amalgamation of regional police organizations into larger or single units. Scotland is a case in point, its eight regional services becoming one Police Scotland in April 2013. Although the reform process was relatively consensual, the new organization has been the subject of numerous controversies, some of which reflect an actual or perceived loss of the local in Scottish policing. Drawing on a qualitative study of the emerging local governance arrangements, we explore the negotiated character of large-scale organizational reform, demonstrating that it is best understood as a process not an event. We also argue that appeals to localism are not mere expressions of sentiment and resistance to change. They reflect the particular historical development of policing and public service delivery in Scotland at the level of municipal government, but also strong convictions that policing should be subject to democratic deliberation and should recognize and be responsive to those subject to it – what we argue here are necessary functions of police governance in general

Optically trapped bacteria pairs reveal discrete motile response to control aggregation upon cell–cell approach

Aggregation of bacteria plays a key role in the formation of many biofilms. The critical first step is cell–cell approach, and yet the ability of bacteria to control the likelihood of aggregation during this primary phase is unknown. Here, we use optical tweezers to measure the force between isolated Bacillus subtilis cells during approach. As we move the bacteria towards each other, cell motility (bacterial swimming) initiates the generation of repulsive forces at bacterial separations of ~3 μm. Moreover, the motile response displays spatial sensitivity with greater cell–cell repulsion evident as inter-bacterial distances decrease. To examine the environmental influence on the inter-bacterial forces, we perform the experiment with bacteria suspended in Tryptic Soy Broth, NaCl solution and deionised water. Our experiments demonstrate that repulsive forces are strongest in systems that inhibit biofilm formation (Tryptic Soy Broth), while attractive forces are weak and rare, even in systems where biofilms develop (NaCl solution). These results reveal that bacteria are able to control the likelihood of aggregation during the approach phase through a discretely modulated motile response. Clearly, the force-generating motility we observe during approach promotes biofilm prevention, rather than biofilm formation

Management of chemotherapy-associated febrile neutropenia

The development of febrile neutropenia during a course of chemotherapy is not only a life-threatening complication, it can also lead to a decision to reduce chemotherapy intensity in subsequent treatment cycles, thus putting patient outcomes at risk. Although there are strategies available for the primary prevention of febrile neutropenia, these are not widely used in the UK management of breast cancer. It is, therefore, paramount to have a well thought out and rigorously implemented care protocol for febrile neutropenia, involving patients, family/carers and health-care professionals in both primary and secondary care, to ensure early detection and effective management

Patterns of sugar-sweetened beverage consumption amongst young people aged 13–15 years during the school day in Scotland

© 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Background There is currently little research regarding sugar-sweetened beverage (SSB) consumption patterns of young people though adolescents are thought to be frequent consumers of these drinks. There is no research regarding the other foods and drinks consumed alongside SSBs by young people. The aim of this paper is to explore the patterns of SSB purchase and consumption amongst young people aged 13–15 years. Methods A purchasing recall questionnaire (PRQ) was administered online in seven case study schools with 535 young people aged 13–15 years. Nutrient composition (kilocalories, fat, saturated fat, sodium and sugar) was also calculated for food/drink purchases. Chi-Square and Wilcoxon-Mann Whitney tests were conducted to examine patterns of SSB consumption and sugar/kilocalories consumption for SSB consumers and non-consumers. Results SSB consumers were significantly more likely to consume a drink at mid-morning break. Fewer consumed food at mid-morning break, ate food before school or ate food at lunchtime, but this was not statistically significant. A higher percentage of SSB consumers consumed ‘unhealthy’ food and drinks in comparison to young people who did not consume a SSB. Both median lunchtime sugar consumption (40.7 g vs 10.2 g) and median sugar as a percentage of Kcals (39% vs 14%) were significantly higher for SSB purchasers in comparison to non-purchasers. Conclusion The analysis highlights that SSB purchasers consume significantly more sugar at lunchtime than non-purchasers. However, both purchasers and non-purchasers exceeded WHO (2015) recommendations that sugar consumption be halved to form no more than 5% of daily energy intake. This study provides new insights for public health stakeholders and schools. Multifaceted and inventive strategies relevant to young people will be required to WHO recommendations.Peer reviewedFinal Published versio

Systematic Analysis of Cell Cycle Effects of Common Drugs Leads to the Discovery of a Suppressive Interaction between Gemfibrozil and Fluoxetine

Screening chemical libraries to identify compounds that affect overall cell proliferation is common. However, in most cases, it is not known whether the compounds tested alter the timing of particular cell cycle transitions. Here, we evaluated an FDA-approved drug library to identify pharmaceuticals that alter cell cycle progression in yeast, using DNA content measurements by flow cytometry. This approach revealed strong cell cycle effects of several commonly used pharmaceuticals. We show that the antilipemic gemfibrozil delays initiation of DNA replication, while cells treated with the antidepressant fluoxetine severely delay progression through mitosis. Based on their effects on cell cycle progression, we also examined cell proliferation in the presence of both compounds. We discovered a strong suppressive interaction between gemfibrozil and fluoxetine. Combinations of interest among diverse pharmaceuticals are difficult to identify, due to the daunting number of possible combinations that must be evaluated. The novel interaction between gemfibrozil and fluoxetine suggests that identifying and combining drugs that show cell cycle effects might streamline identification of drug combinations with a pronounced impact on cell proliferation

Use of recommended medications after myocardial infarction in Austria

Guidelines recommend long-term use of beta-blockers (BB), statins, and angiotensin-converting-enzyme-inhibitors or angiotensin-receptor-blockers (ACEI/ARB) after myocardial infarction (MI), but data on their use after discharge are scarce. From Austrian sickness funds claims, we identified all acute MI patients who were discharged within 30 days and who survived ≥120 days after MI in 2004. We ascertained outpatient use of ACEI/ARBs, BBs, statins, and aspirin from all filled prescriptions between discharge and 120 days post MI. Comorbidities were ascertained from use of indicator drugs during the preceding year. Multivariate logistic regression was used to evaluate the independent determinants of study drug use. We evaluated 4,105 MI patients, whose mean age was 68.8 (±13.2) years; 59.5% were men. Within 120 days after MI, 67% filled prescriptions for ACE/ARBs, 74% for BBs, and 67% for statin. While 41% received all these classes and 34% two, 25% of patients received only one or none of these drugs. Older age and presence of severe mental illness were associated with lower use of all drug classes. Diabetics had greater ACEI/ARB use. Fewer BBs were used in patients with obstructive lung disease. Statin use was lower in patients using treatment for congestive heart failure (all P < 0.001). We conclude that recommended medications were underused in Austrian MI survivors. Quality indicators should be established and interventions be implemented to ensure maximum secondary prevention after MI

Is diagnosing exposed dentine a suitable tool for grading erosive loss?

Quantifying tooth wear in general and erosion in particular mostly is made by distinguishing between lesions restricted to enamel and lesions reaching the underlying dentine. Various scores for grading have been used, but in all systems, higher scores are given in cases of exposed dentine, thus, indicating a more severe stage of the condition. Clinical diagnosis of exposed dentine is made by assessing changes in colour or optical properties of the hard tissues. This paper aims to review the literature and discuss critically problems arising form this approach. It appears that classifying the severity of erosion by the area or depth of exposed dentine is difficult and poorly reproducible, and taking into account the variation of enamel thickness, the amount of tissue lost often is not related simply to the area of exposed dentine. There has still been very little longitudinal investigation of the significance of exposed dentine as a prognostic indicator. Further work and discussion is needed to reevaluate the explanative power of current grading procedures