Evolution of mitochondrial and nuclear genomes in Pennatulacea

We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens

Sediment-rich meltwater plumes and ice-proximal fans at the margins of modern and ancient tidewater glaciers: Observations and modeling

Turbid meltwater plumes and ice-proximal fans occur where subglacial streams reach the grounded marine margins of modern and ancient tidewater glaciers. However, the spacing and temporal stability of these subglacial channels is poorly understood. This has significant implications for understanding the geometry and distribution of Quaternary and ancient ice-proximal fans that can form important aquifers and hydrocarbon reservoirs. Remote-sensing and numerical-modelling techniques are applied to the 200 km-long marine margin of a Svalbard ice cap, Austfonna, to quantify turbid meltwaterplume distribution and predict its temporal stability. Results are combined with observations from geophysical data close to the modern ice front to refine existing depositional models for ice-proximal fans. Plumes are spaced about 3 km apart and their distribution along the ice front is stable over decades. Numerical modelling also predicts the drainage pattern and meltwater discharge beneath the ice cap; modelled water-routing patterns are in reasonable agreement with satellite-mapped plume locations. However, glacial retreat of several kilometres over the past 40 years has limited build-up of significant ice-proximal fans. A single fan and moraine ridge is noted from marine-geophysical surveys. Closer to the ice front there are smaller recessional moraines and polygonal sediment lobes but no identifiable fans. Schematic models of ice-proximal deposits represent varying glacierterminus stability: (i) stable terminus where meltwater sedimentation produces an ice-proximal fan; (ii) quasi-stable terminus, where glacier readvance pushes or thrusts up ice-proximal deposits into a morainal bank; (iii) retreating terminus, with short still-stands, allowing only small sediment lobes to build up at melt-stream portals. These modern investigations are complemented with outcrop and subsurface observations and numerical modelling of an ancient, Ordovician glacial system. Thick turbidite successions and large fans in the Late Ordovician suggest either high-magnitude events or sustained high discharge, consistent with a relatively mild palaeo-glacial setting.We thank BP Algeria for sponsorship, Ed Jones and Liz Jolley of BP for supporting the project.This is the accepted manuscript. The final published version is available from Wiley at http://dx.doi.org/10.1111/sed.1219

Phylogenetics and Mitogenome Organisation in Black Corals (Anthozoa: Hexacorallia: Antipatharia): An Order-Wide Survey Inferred From Complete Mitochondrial Genomes

Black corals (Anthozoa: Antipatharia) are an ecologically and culturally important group of deep-sea cnidarians. However, as the majority of species inhabit depths >50 m, they are relatively understudied. The inaccessibility of well-preserved tissue for species of interest has limited the scope of molecular analysis, and as a result only a small number of antipatharian mitochondrial genomes have been published. Using next generation sequencing, 18 complete and five partial antipatharian mitochondrial genomes were assembled, increasing the number of complete mitochondrial genomes to 22. This includes species from six antipatharian families, four of which were previously unrepresented, enabling the first family-level, full mitochondrial gene analysis over the whole order. The circular mitogenomes ranged in size from 17,681 to 21,669 bp with the large range in size due to the addition of an intron in COX1 in some species and size variation of intergenic regions. All mitogenomes contained the genes standard to all hexacoral mitogenomes (13 protein coding genes, two rRNAs and two tRNAs). The only difference in gene content is the presence of the COX1 intron in five families. The most variable mitochondrial gene is ND4 which may have implications for future barcoding studies. Phylogenetic analysis confirms that Leiopathidae is sister to all other families. Families Antipathidae, Cladopathidae and Schizopathidae are polyphyletic, supporting previous studies that call for a taxonomic revision

Prioritizing single-nucleotide variations that potentially regulate alternative splicing

Recent evidence suggests that many complex diseases are caused by genetic variations that play regulatory roles in controlling gene expression. Most genetic studies focus on nonsynonymous variations that can alter the amino acid composition of a protein and are therefore believed to have the highest impact on phenotype. Synonymous variations, however, can also play important roles in disease pathogenesis by regulating pre-mRNA processing and translational control. In this study, we systematically survey the effects of single-nucleotide variations (SNVs) on binding affinity of RNA-binding proteins (RBPs). Among the 10,113 synonymous SNVs identified in 697 individuals in the 1,000 Genomes Project and distributed by Genetic Analysis Workshop 17 (GAW17), we identified 182 variations located in alternatively spliced exons that can significantly change the binding affinity of nine RBPs whose binding preferences on 7-mer RNA sequences were previously reported. We found that the minor allele frequencies of these variations are similar to those of nonsynonymous SNVs, suggesting that they are in fact functional. We propose a workflow to identify phenotype-associated regulatory SNVs that might affect alternative splicing from exome-sequencing-derived genetic variations. Based on the affecting SNVs on the quantitative traits simulated in GAW17, we further identified two and four functional SNVs that are predicted to be involved in alternative splicing regulation in traits Q1 and Q2, respectively

Estimating the Location and Spatial Extent of a Covert Anthrax Release

Rapidly identifying the features of a covert release of an agent such as anthrax could help to inform the planning of public health mitigation strategies. Previous studies have sought to estimate the time and size of a bioterror attack based on the symptomatic onset dates of early cases. We extend the scope of these methods by proposing a method for characterizing the time, strength, and also the location of an aerosolized pathogen release. A back-calculation method is developed allowing the characterization of the release based on the data on the first few observed cases of the subsequent outbreak, meteorological data, population densities, and data on population travel patterns. We evaluate this method on small simulated anthrax outbreaks (about 25–35 cases) and show that it could date and localize a release after a few cases have been observed, although misspecifications of the spore dispersion model, or the within-host dynamics model, on which the method relies can bias the estimates. Our method could also provide an estimate of the outbreak's geographical extent and, as a consequence, could help to identify populations at risk and, therefore, requiring prophylactic treatment. Our analysis demonstrates that while estimates based on the first ten or 15 observed cases were more accurate and less sensitive to model misspecifications than those based on five cases, overall mortality is minimized by targeting prophylactic treatment early on the basis of estimates made using data on the first five cases. The method we propose could provide early estimates of the time, strength, and location of an aerosolized anthrax release and the geographical extent of the subsequent outbreak. In addition, estimates of release features could be used to parameterize more detailed models allowing the simulation of control strategies and intervention logistics

Problems in dealing with missing data and informative censoring in clinical trials

A common problem in clinical trials is the missing data that occurs when patients do not complete the study and drop out without further measurements. Missing data cause the usual statistical analysis of complete or all available data to be subject to bias. There are no universally applicable methods for handling missing data. We recommend the following: (1) Report reasons for dropouts and proportions for each treatment group; (2) Conduct sensitivity analyses to encompass different scenarios of assumptions and discuss consistency or discrepancy among them; (3) Pay attention to minimize the chance of dropouts at the design stage and during trial monitoring; (4) Collect post-dropout data on the primary endpoints, if at all possible; and (5) Consider the dropout event itself an important endpoint in studies with many

Inducible and constitutive heat shock gene expression responds to modification of Hsp70 copy number in Drosophila melanogaster but does not compensate for loss of thermotolerance in Hsp70 null flies

<p>Abstract</p> <p>Background</p> <p>The heat shock protein Hsp70 promotes inducible thermotolerance in nearly every organism examined to date. Hsp70 interacts with a network of other stress-response proteins, and dissecting the relative roles of these interactions in causing thermotolerance remains difficult. Here we examine the effect of <it>Hsp70 </it>gene copy number modification on thermotolerance and the expression of multiple stress-response genes in <it>Drosophila melanogaster</it>, to determine which genes may represent mechanisms of stress tolerance independent of Hsp70.</p> <p>Results</p> <p><it>Hsp70 </it>copy number in four strains is positively associated with <it>Hsp70 </it>expression and inducible thermotolerance of severe heat shock. When assayed at carefully chosen temperatures, <it>Hsp70 </it>null flies are almost entirely deficient in thermotolerance. In contrast to expectations, increasing <it>Hsp70 </it>expression levels induced by thermal pretreatment are associated with increasing levels of seven other inducible <it>Hsps </it>across strains. In addition, complete <it>Hsp70 </it>loss causes upregulation of the inducible <it>Hsps </it>and six constitutive stress-response genes following severe heat shocks.</p> <p>Conclusion</p> <p>Modification of <it>Hsp70 </it>copy number quantitatively and qualitatively affects the expression of multiple other stress-response genes. A positive association between absolute expression levels of <it>Hsp70 </it>and other <it>Hsps </it>after thermal pretreatment suggests novel regulatory mechanisms. Severe heat shocks induce both novel gene expression patterns and almost total mortality in the <it>Hsp70 </it>null strain: alteration of gene expression in this strain does not compensate for <it>Hsp70 </it>loss but suggests candidates for overexpression studies.</p

Inhibition of SOC/Ca2+/NFAT pathway is involved in the anti-proliferative effect of sildenafil on pulmonary artery smooth muscle cells

<p>Abstract</p> <p>Background</p> <p>Sildenafil, a potent phosphodiesterase type 5 (PDE5) inhibitor, has been proposed as a treatment for pulmonary arterial hypertension (PAH). The mechanism of its anti-proliferative effect on pulmonary artery smooth muscle cells (PASMC) is unclear. Nuclear translocation of nuclear factor of activated T-cells (NFAT) is thought to be involved in PASMC proliferation and PAH. Increase in cytosolic free [Ca²⁺] ([Ca²⁺]_i) is a prerequisite for NFAT nuclear translocation. Elevated [Ca²⁺]_iin PASMC of PAH patients has been demonstrated through up-regulation of store-operated Ca²⁺channels (SOC) which is encoded by the transient receptor potential (TRP) channel protein. Thus we investigated if: 1) up-regulation of TRPC1 channel expression which induces enhancement of SOC-mediated Ca²⁺influx and increase in [Ca²⁺]_iis involved in hypoxia-induced PASMC proliferation; 2) hypoxia-induced promotion of [Ca²⁺]_ileads to nuclear translocation of NFAT and regulates PASMC proliferation and TRPC1 expression; 3) the anti-proliferative effect of sildenafil is mediated by inhibition of this SOC/Ca²⁺/NFAT pathway.</p> <p>Methods</p> <p>Human PASMC were cultured under hypoxia (3% O₂) with or without sildenafil treatment for 72 h. Cell number and cell viability were determined with a hemocytometer and MTT assay respectively. [Ca²⁺]_iwas measured with a dynamic digital Ca²⁺imaging system by loading PASMC with fura 2-AM. TRPC1 mRNA and protein level were detected by RT-PCR and Western blotting respectively. Nuclear translocation of NFAT was determined by immunofluoresence microscopy.</p> <p>Results</p> <p>Hypoxia induced PASMC proliferation with increases in basal [Ca²⁺]_iand Ca²⁺entry via SOC (SOCE). These were accompanied by up-regulation of TRPC1 gene and protein expression in PASMC. NFAT nuclear translocation was significantly enhanced by hypoxia, which was dependent on SOCE and sensitive to SOC inhibitor SKF96365 (SKF), as well as cGMP analogue, 8-brom-cGMP. Hypoxia-induced PASMC proliferation and TRPC1 up-regulation were inhibited by SKF and NFAT blocker (VIVIT and Cyclosporin A). Sildenafil treatment ameliorated hypoxia-induced PASMC proliferation and attenuated hypoxia-induced enhancement of basal [Ca²⁺]_i, SOCE, up-regulation of TRPC1 expression, and NFAT nuclear translocation.</p> <p>Conclusion</p> <p>The SOC/Ca²⁺/NFAT pathway is, at least in part, a downstream mediator for the anti-proliferative effect of sildenafil, and may have therapeutic potential for PAH treatment.</p

Lens stem cells may reside outside the lens capsule: an hypothesis

In this paper, we consider the ocular lens in the context of contemporary developments in biological ideas. We attempt to reconcile lens biology with stem cell concepts and a dearth of lens tumors

Testosterone levels are negatively associated with childlessness in males, but positively related to offspring count in fathers

Variation in testosterone (T) is thought to affect the allocation of effort between reproductive and parenting strategies. Here, using a large sample of elderly American men (n = 754) and women (n = 669) we examined the relationship between T and self-reported parenthood, as well as the relationship between T and number of reported children. Results supported previous findings from the literature, showing that fathers had lower T levels than men who report no children. Furthermore, we found that among fathers T levels were positively associated with the number of children a man reports close to the end of his lifespan. Results were maintained when controlling for a number of relevant factors such as time of T sampling, participant age, educational attainment, BMI, marital status and reported number of sex partners. In contrast, T was not associated with either motherhood or the number of children women had, suggesting that, at least in this sample, T does not influence the allocation of effort between reproductive and parenting strategies among women. Findings from this study contribute to the growing body of literature suggesting that, among men, pair bonding and paternal care are associated with lower T levels, while searching and acquiring sex partners is associated with higher T levels.27 Jun 2013: Pollet TV, Cobey KD, van der Meij L (2013) Correction: Testosterone Levels Are Negatively Associated with Childlessness in Males, but Positively Related to Offspring Count in Fathers. PLoS ONE 8(6): 10.1371/annotation/bccccb7e-48a7-4594-b3e6-ce8c9d2489a2