Fossils and living taxa agree on patterns of body mass evolution:A case study with Afrotheria

Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns

Empirical study of correlated survival times for recurrent events with proportional hazards margins and the effect of correlation and censoring.

Background: In longitudinal studies where subjects experience recurrent incidents over a period of time, such as respiratory infections, fever or diarrhea, statistical methods are required to take into account the within-subject correlation. Methods: For repeated events data with censored failure, the independent increment (AG), marginal (WLW) and conditional (PWP) models are three multiple failure models that generalize Cox"s proportional hazard model. In this paper, we revise the efficiency, accuracy and robustness of all three models under simulated scenarios with varying degrees of within-subject correlation, censoring levels, maximum number of possible recurrences and sample size. We also study the methods performance on a real dataset from a cohort study with bronchial obstruction. Results: We find substantial differences between methods and there is not an optimal method. AG and PWP seem to be preferable to WLW for low correlation levels but the situation reverts for high correlations. Conclusions: All methods are stable in front of censoring, worsen with increasing recurrence levels and share a bias problem which, among other consequences, makes asymptotic normal confidence intervals not fully reliable, although they are well developed theoretically

Livestock trade networks for guiding animal health surveillance

BACKGROUND: Trade in live animals can contribute to the introduction of exotic diseases, the maintenance and spread endemic diseases. Annually millions of animals are moved across Europe for the purposes of breeding, fattening and slaughter. Data on the number of animals moved were obtained from the Directorate General Sanco (DG Sanco) for 2011. These were converted to livestock units to enable direct comparison across species and their movements were mapped, used to calculate the indegrees and outdegrees of 27 European countries and the density and transitivity of movements within Europe. This provided the opportunity to discuss surveillance of European livestock movement taking into account stopping points en-route. RESULTS: High density and transitivity of movement for registered equines, breeding and fattening cattle, breeding poultry and pigs for breeding, fattening and slaughter indicates that hazards have the potential to spread quickly within these populations. This is of concern to highly connected countries particularly those where imported animals constitute a large proportion of their national livestock populations, and have a high indegree. The transport of poultry (older than 72 hours) and unweaned animals would require more rest breaks than the movement of weaned animals, which may provide more opportunities for disease transmission. Transitivity is greatest for animals transported for breeding purposes with cattle, pigs and poultry having values of over 50%. CONCLUSIONS: This paper demonstrated that some species (pigs and poultry) are traded much more frequently and at a larger scale than species such as goats. Some countries are more vulnerable than others due to importing animals from many countries, having imported animals requiring rest-breaks and importing large proportions of their national herd or flock. Such knowledge about the vulnerability of different livestock systems related to trade movements can be used to inform the design of animal health surveillance systems to facilitate the trade in animals between European member states. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0354-4) contains supplementary material, which is available to authorized users

Distinct Mechanisms for Induction and Tolerance Regulate the Immediate Early Genes Encoding Interleukin 1β and Tumor Necrosis Factor α

Interleukin-1β and Tumor Necrosis Factor α play related, but distinct, roles in immunity and disease. Our study revealed major mechanistic distinctions in the Toll-like receptor (TLR) signaling-dependent induction for the rapidly expressed genes (IL1B and TNF) coding for these two cytokines. Prior to induction, TNF exhibited pre-bound TATA Binding Protein (TBP) and paused RNA Polymerase II (Pol II), hallmarks of poised immediate-early (IE) genes. In contrast, unstimulated IL1B displayed very low levels of both TBP and paused Pol II, requiring the lineage-specific Spi-1/PU.1 (Spi1) transcription factor as an anchor for induction-dependent interaction with two TLR-activated transcription factors, C/EBPβ and NF-κB. Activation and DNA binding of these two pre-expressed factors resulted in de novo recruitment of TBP and Pol II to IL1B in concert with a permissive state for elongation mediated by the recruitment of elongation factor P-TEFb. This Spi1-dependent mechanism for IL1B transcription, which is unique for a rapidly-induced/poised IE gene, was more dependent upon P-TEFb than was the case for the TNF gene. Furthermore, the dependence on phosphoinositide 3-kinase for P-TEFb recruitment to IL1B paralleled a greater sensitivity to the metabolic state of the cell and a lower sensitivity to the phenomenon of endotoxin tolerance than was evident for TNF. Such differences in induction mechanisms argue against the prevailing paradigm that all IE genes possess paused Pol II and may further delineate the specific roles played by each of these rapidly expressed immune modulators. © 2013 Adamik et al

International Delegations and the Values of Federalism

Inland water sediments receive large quantities of terrestrial organic matter(1-5) and are globally important sites for organic carbon preservation(5,6). Sediment organic matter mineralization is positively related to temperature across a wide range of high-latitude ecosystems(6-10), but the situation in the tropics remains unclear. Here we assessed temperature effects on the biological production of CO2 and CH4 in anaerobic sediments of tropical lakes in the Amazon and boreal lakes in Sweden. On the basis of conservative regional warming projections until 2100 (ref. 11), we estimate that sediment CO2 and CH4 production will increase 9-61% above present rates. Combining the CO2 and CH4 as CO2 equivalents (CO(2)eq; ref. 11), the predicted increase is 2.4-4.5 times higher in tropical than boreal sediments. Although the estimated lake area in low latitudes is 3.2 times smaller than that of the boreal zone, we estimate that the increase in gas production from tropical lake sediments would be on average 2.4 times higher for CO2 and 2.8 times higher for CH4. The exponential temperature response of organic matter mineralization, coupled with higher increases in the proportion of CH4 relative to CO2 on warming, suggests that the production of greenhouse gases in tropical sediments will increase substantially. This represents a potential large-scale positive feedback to climate change

Enucleation and development of cluster headache: a retrospective study

BACKGROUND: Cluster headache (CH) is a neurovascular, primary headache disorder. There are, however, several case reports about patients whose CH started shortly after a structural brain disease or trauma. Motivated by a patient who developed CH 3 weeks after the removal of an eye and by similar case reports, we tested the hypothesis that the removal of an eye is a risk factor for CH. METHODS: A detailed headache questionnaire was filled out by 112 patients on average 8 years after enucleation or evisceration of an eye. RESULTS: While 21 % of these patients experienced previously unknown headaches after the removal of an eye, no patient fulfilled the diagnostic criteria for CH. CONCLUSION: Our data does not suggest that the removal of an eye is a major risk factor for the development of CH

No evidence that footedness in pheasants influences cognitive performance in tasks assessing colour discrimination and spatial ability

The differential specialization of each side of the brain facilitates the parallel processing of information and has been documented in a wide range of animals. Animals that are more lateralized as indicated by consistent preferential limb use are commonly reported to exhibit superior cognitive ability as well as other behavioural advantages.We assayed the lateralization of 135 young pheasants (Phasianus colchicus), indicated by their footedness in a spontaneous stepping task, and related this measure to individual performance in either 3 assays of visual or spatial learning and memory. We found no evidence that pronounced footedness enhances cognitive ability in any of the tasks. We also found no evidence that an intermediate footedness relates to better cognitive performance. This lack of relationship is surprising because previous work revealed that pheasants have a slight population bias towards right footedness, and when released into the wild, individuals with higher degrees of footedness were more likely to die. One explanation for why extreme lateralization is constrained was that it led to poorer cognitive performance, or that optimal cognitive performance was associated with some intermediate level of lateralization. This stabilizing selection could explain the pattern of moderate lateralization that is seen in most non-human species that have been studied. However, we found no evidence in this study to support this explanation

Evaluating the association of common APOA2 variants with type 2 diabetes

<p>Abstract</p> <p>Background</p> <p><it>APOA2 </it>is a positional and biological candidate gene for type 2 diabetes at the chromosome 1q21-q24 susceptibility locus. The aim of this study was to examine if HapMap phase II tag SNPs in <it>APOA2 </it>are associated with type 2 diabetes and quantitative traits in French Caucasian subjects.</p> <p>Methods</p> <p>We genotyped the three HapMap phase II tagging SNPs (rs6413453, rs5085 and rs5082) required to capture the common variation spanning the <it>APOA2 </it>locus in our type 2 diabetes case-control cohort comprising 3,093 French Caucasian subjects. The association between these variants and quantitative traits was also examined in the normoglycaemic adults of the control cohort. In addition, meta-analysis of publicly available whole genome association data was performed.</p> <p>Results</p> <p>None of the <it>APOA2 </it>tag SNPs were associated with type 2 diabetes in the French Caucasian case-control cohort (rs6413453, <it>P </it>= 0.619; rs5085, <it>P </it>= 0.245; rs5082, <it>P </it>= 0.591). However, rs5082 was marginally associated with total cholesterol levels (<it>P </it>= 0.026) and waist-to-hip ratio (<it>P </it>= 0.029). The meta-analysis of data from 12,387 subjects confirmed our finding that common variation at the <it>APOA2 </it>locus is not associated with type 2 diabetes.</p> <p>Conclusion</p> <p>The available data does not support a role for common variants in <it>APOA2 </it>on type 2 diabetes susceptibility or related quantitative traits in Northern Europeans.</p

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. There are multiple published methods for strand-specific RNA-seq, but no consensus exists as to how to choose between them. Here we developed a comprehensive computational pipeline to compare library quality metrics from any RNA-seq method. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library-construction protocols, including both published and our own methods. We found marked differences in strand specificity, library complexity, evenness and continuity of coverage, agreement with known annotations and accuracy for expression profiling. Weighing each method's performance and ease, we identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms.Howard Hughes Medical InstituteUnited States-Israel Binational Science Foundatio

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

<p>Abstract</p> <p>Background</p> <p>Initiation and elongation of RNA polymerase II (RNAPII) transcription is regulated by both DNA sequence and chromatin signals. Recent breakthroughs make it possible to measure the chromatin state and activity of core promoters genome-wide, but dedicated computational strategies are needed to progress from descriptive annotation of data to quantitative, predictive models.</p> <p>Results</p> <p>Here, we describe a computational framework which with high accuracy can predict the locations of core promoters, the amount of recruited RNAPII at the promoter, the amount of elongating RNAPII in the gene body, the mRNA production originating from the promoter and finally also the stalling characteristics of RNAPII by considering both quantitative and spatial features of histone modifications around the transcription start site (TSS).</p> <p>As the model framework can also pinpoint the signals that are the most influential for prediction, it can be used to infer underlying regulatory biology. For example, we show that the H3K4 di- and tri- methylation signals are strongly predictive for promoter location while the acetylation marks H3K9 and H3K27 are highly important in estimating the promoter usage. All of these four marks are found to be necessary for recruitment of RNAPII but not sufficient for the elongation. We also show that the spatial distributions of histone marks are almost as predictive as the signal strength and that a set of histone marks immediately downstream of the TSS is highly predictive of RNAPII stalling.</p> <p>Conclusions</p> <p>In this study we introduce a general framework to accurately predict the level of RNAPII recruitment, elongation, stalling and mRNA expression from chromatin signals. The versatility of the method also makes it ideally suited to investigate other genomic data.</p