MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEv​al/downloads

Evaluation of corrective measures implemented for the preventive conservation of fresco paintings in Ariadne s house (Pompeii, Italy)

BACKGROUND: A microclimate monitoring study was conducted in 2008 aimed at assessing the conservation risks affecting the valuable wall paintings decorating Ariadne s House (Pompeii, Italy). It was found that thermohygrometric conditions were very unfavorable for the conservation of frescoes. As a result, it was decided to implement corrective measures, and the transparent polycarbonate sheets covering three rooms (one of them delimited by four walls and the others composed of three walls) were replaced by opaque roofs. In order to examine the effectiveness of this measure, the same monitoring system comprised by 26 thermohygrometric probes was installed again in summer 2010. Data recorded in 2008 and 2010 were compared. RESULTS: Microclimate conditions were also monitored in a control room with the same roof in both years. The average temperature in this room was lower in 2010, and it was decided to consider a time frame of 18 summer days with the same mean temperature in both years. In the rooms with three walls, the statistical analysis revealed that the diurnal maximum temperature decreased about 3.5 ºC due to the roof change, and the minimum temperature increased 0.5 ºC. As a result, the daily thermohygrometric variations resulted less pronounced in 2010, with a reduction of approximately 4 ºC, which is favorable for the preservation of mural paintings. In the room with four walls, the daily fluctuations also decreased about 4 ºC. Based on the results, other alternative actions are discussed aimed at improving the conservation conditions of wall paintings. CONCLUSIONS: The roof change has reduced the most unfavorable thermohygrometric conditions affecting the mural paintings, but additional actions should be adopted for a long term preservation of Pompeian frescoes.This work was partially supported by the Spanish Government (Ministerio de Ciencia e Innovacion) under projects HAR2010-21944-C02-01 and HAR2010-21944-C02-02.Merello Giménez, P.; García Diego, FJ.; Zarzo Castelló, M. (2013). Evaluation of corrective measures implemented for the preventive conservation of fresco paintings in Ariadne s house (Pompeii, Italy). Chemistry Central Journal. 7(1):87-87. doi:10.1186/1752-153X-7-87S878771DELOSRIOS, A., CAMARA, B., GARCIADELCURA, M., RICO, V., GALVAN, V., & ASCASO, C. (2009). Deteriorating effects of lichen and microbial colonization of carbonate building rocks in the Romanesque churches of Segovia (Spain). Science of The Total Environment, 407(3), 1123-1134. doi:10.1016/j.scitotenv.2008.09.042Nava, S., Becherini, F., Bernardi, A., Bonazza, A., Chiari, M., García-Orellana, I., … Vecchi, R. (2010). An integrated approach to assess air pollution threats to cultural heritage in a semi-confined environment: The case study of Michelozzo’s Courtyard in Florence (Italy). Science of The Total Environment, 408(6), 1403-1413. doi:10.1016/j.scitotenv.2009.07.03

Upregulation of PPARβ/δ Is Associated with Structural and Functional Changes in the Type I Diabetes Rat Diaphragm

Diabetes mellitus is associated with alterations in peripheral striated muscles and cardiomyopathy. We examined diaphragmatic function and fiber composition and identified the role of peroxisome proliferator-activated receptors (PPAR alpha and beta/delta) as a factor involved in diaphragm muscle plasticity in response to type I diabetes.Streptozotocin-treated rats were studied after 8 weeks and compared with their controls. Diaphragmatic strips were stimulated in vitro and mechanical and energetic variables were measured, cross bridge kinetics assessed, and the effects of fatigue and hypoxia evaluated. Morphometry, myosin heavy chain isoforms, PPAR alpha and beta/delta gene and protein expression were also assessed. Diabetes induced a decrease in maximum velocity of shortening (-14%, P<0.05) associated with a decrease in myosin ATPase activity (-49%, P<0.05), and an increase in force (+20%, P<0.05) associated with an increase in the number of cross bridges (+14%, P<0.05). These modifications were in agreement with a shift towards slow myosin heavy chain fibers and were associated with an upregulation of PPARbeta/delta (+314% increase in gene and +190% increase in protein expression, P<0.05). In addition, greater resistances to fatigue and hypoxia were observed in diabetic rats.Type I diabetes induced complex mechanical and energetic changes in the rat diaphragm and was associated with an up-regulation of PPARbeta/delta that could improve resistance to fatigue and hypoxia and favour the shift towards slow myosin heavy chain isoforms

Burden of Disease Caused by Otitis Media: Systematic Review and Global Estimates

<div><h3>Background</h3><p>Otitis media (OM) is a leading cause of health care visits and drugs prescription. Its complications and sequelae are important causes of preventable hearing loss, particularly in developing countries. Within the Global Burden of Diseases, Injuries, and Risk Factors Study, for the year 2005 we estimated the incidence of acute OM, chronic suppurative OM, and related hearing loss and mortality for all ages and the 21 WHO regional areas.</p> <h3>Methods</h3><p>We identified risk factors, complications and sequelae of OM. We carried out an extensive literature review (Medline, Embase, Lilacs and Wholis) which lead to the selection of 114 papers comprising relevant data. Data were available from 15 of the 21 WHO regions. To estimate incidence and prevalence for all countries we adopted a two stage approach based on risk factors formulas and regression modelling.</p> <h3>Results</h3><p>Acute OM incidence rate is 10.85% i.e. 709million cases each year with 51% of these occurring in under-fives. Chronic suppurative OM incidence rate is 4.76‰ i.e. 31million cases, with 22.6% of cases occurring annually in under-fives. OM-related hearing impairment has a prevalence of 30.82 per ten-thousand. Each year 21thousand people die due to complications of OM.</p> <h3>Conclusions</h3><p>Our study is the first attempt to systematically review the available information and provide global estimates for OM and related conditions. The overall burden deriving from AOM, CSOM and their sequelae is considerable, particularly in the first five years of life and in the poorest countries. The findings call for incorporating OM-focused action within preventive and case management strategies, with emphasis on the more affected.</p> </div

Emergence and Genetic Variation of Neuraminidase Stalk Deletions in Avian Influenza Viruses

When avian influenza viruses (AIVs) are transmitted from their reservoir hosts (wild waterfowl and shorebirds) to domestic bird species, they undergo genetic changes that have been linked to higher virulence and broader host range. Common genetic AIV modifications in viral proteins of poultry isolates are deletions in the stalk region of the neuraminidase (NA) and additions of glycosylation sites on the hemagglutinin (HA). Even though these NA deletion mutations occur in several AIV subtypes, they have not been analyzed comprehensively. In this study, 4,920 NA nucleotide sequences, 5,596 HA nucleotide and 4,702 HA amino acid sequences were analyzed to elucidate the widespread emergence of NA stalk deletions in gallinaceous hosts, the genetic polymorphism of the deletion patterns and association between the stalk deletions in NA and amino acid variants in HA. Forty-seven different NA stalk deletion patterns were identified in six NA subtypes, N1–N3 and N5–N7. An analysis that controlled for phylogenetic dependence due to shared ancestry showed that NA stalk deletions are statistically correlated with gallinaceous hosts and certain amino acid features on the HA protein. Those HA features included five glycosylation sites, one insertion and one deletion. The correlations between NA stalk deletions and HA features are HA-NA-subtype-specific. Our results demonstrate that stalk deletions in the NA proteins of AIV are relatively common. Understanding the NA stalk deletion and related HA features may be important for vaccine and drug development and could be useful in establishing effective early detection and warning systems for the poultry industry

Childhood emotional trauma and cyberbullying perpetration among emerging adults: a multiple mediation model of the role of problematic social media use and psychopathology

Research suggests that a small minority of social media users experience problems as a result of their online use. The purpose of the present study was to examine the association of cyberbullying perpetration and problematic social media use with childhood emotional trauma, Cluster B (narcissistic, histrionic, antisocial, and borderline) personality traits, dissociative experiences (DEs), depression, and self-esteem in a nonclinical undergraduate sample. A total of 344 university students volunteered to complete a questionnaire that included measures on the aforementioned dimensions. Thirty-eight percent of the participants had emotional neglect and 27% had emotional abuse, while 44% of them demonstrated at least one cyberbullying perpetration behavior. Results indicated that cyberbullying perpetrators had higher scores on problematic social media use, dissociative experiences, Cluster B traits, depression and childhood emotional trauma, and lower on self-esteem. Path analysis demonstrated that, while adjusting for gender and age, childhood emotional trauma was directly and indirectly associated with cyberbullying perpetration via Cluster B traits. Moreover, depression and dissociation were directly associated with problematic social media use. The findings of this study emphasize the important direct role of childhood emotional trauma and pathological personality traits on cyberbullying perpetration