Phylogenetic analysis of cytochrome c oxidase I sequences to determine higher-level relationships within the coleoid cephalopods

Until recently, the higher-level phylogenetic relationships of coleoid cephalopods have remained unclear. A thorough knowledge of the higher-level phylogeny of the group has been limited by the paucity of paleontological data for this poorly-fossilized group and the lack of cladistic analyses of developmental, morphological, and molecular data applied to the coleoids. In this study we analyzed a 657 base pair portion of the mitochondrial cytochrome c oxidase I (COI) gene from 48 cephalopod species representing a broad spectrum of coleoid diversity to examine higher-level phylogenetic relationships within the group. The COI gene exhibited a high degree of nucleotide sequence variability, with one half of the sites varying in at least one taxon. COI amino acid sequences were highly conserved, but were useful in determining basal-level relationships among the Coleoidea. The evolutionary rate of COI amino acid sequences differed significantly between the two main lineages. The average amino acid sequence divergence within the Octopodiformes was over twice that of the average divergence within the decapods. In addition to analysis of the unweighted data set, phylogenetic analysis was conducted on the data subjected to a single round of rescaled consistency index (RCI) weighting to reduce the effect of homoplasious substitutions in determining phylogenetic structure. To further reduce the influence of homoplastic change and to facilitate bootstrap analysis of the data, a nested analysis of the data was employed, beginning with an analysis of the entire data set to determine proper outgroups to be used in the more restrictive analysis of the decapods and octopods separately. We draw the following conclusions from our analysis of cephalopod COI sequences: (I) the Coleoidea, Octopoda, Vampyromorpha, and Decapoda are monophyletic groups; (2) the Vampyromorpha and Octopoda are sister groups; (3) the Sepioidea, as including the five families Spirulidae, Sepiolidae, Sepiidae, Sepiadariidae, and Idiosepiidae, is polyphyletic; (4) Spirula is more closely related to the Teuthoidea than it is to the remaining members of the Sepioidea; and (5) the Oegopsida, as currently defined is polyphyletic

Glow discharge in low pressure plasma PVD: mathematical model and numerical simulations

In this paper we analyze the problem of glow discharge in low pressure plasma in industrial plant, for chambers of different shapes and various working parameters, like pressure and electric potential. The model described is based upon a static approximation of the AC configuration with two electrodes and a drift diffusion approximation for the current density of positive ions and electrons. A detailed discussion of the boundary conditions imposed is given, as well as the full description of the mathematical model. Numerical simulations were performed for a simple 1D model and two different 2D models, corresponding to two different settings of the industrial plant. The simpler case consists of a radially symmetric chamber, with one central electrode (cathode), based upon a DC generator. In this case, the steel chamber acts as the anode. The second model concerns a two dimensional horizontal cut of the most common plant configuration, with two electrodes connected to an AC generator. The case is treated in a "quasi-static" approximation. The three models show some common behaviours, particularly including the main expected features, such as dark spaces, glow regions and a wide "plasma region". Furthermore, the three shown models show some similarities with previously published results concerning 1D and simplified 2D models, as well as with some preliminary results of the full 3D case.Comment: 16 pages, 11 figures, in pres

Low-temperature plasma treatment induces DNA damage leading to necrotic cell death in primary prostate epithelial cells

Background:In recent years, the rapidly advancing field of low-temperature atmospheric pressure plasmas has shown considerable promise for future translational biomedical applications, including cancer therapy, through the generation of reactive oxygen and nitrogen species.Method:The cytopathic effect of low-temperature plasma was first verified in two commonly used prostate cell lines: BPH-1 and PC-3 cells. The study was then extended to analyse the effects in paired normal and tumour (Gleason grade 7) prostate epithelial cells cultured directly from patient tissue. Hydrogen peroxide (H2O2) and staurosporine were used as controls throughout.Results:Low-temperature plasma (LTP) exposure resulted in high levels of DNA damage, a reduction in cell viability, and colony-forming ability. H2O2 formed in the culture medium was a likely facilitator of these effects. Necrosis and autophagy were recorded in primary cells, whereas cell lines exhibited apoptosis and necrosis.Conclusions:This study demonstrates that LTP treatment causes cytotoxic insult in primary prostate cells, leading to rapid necrotic cell death. It also highlights the need to study primary cultures in order to gain more realistic insight into patient response

Dystrophic heart failure blocked by membrane sealant poloxamer

Dystrophin deficiency causes Duchenne muscular dystrophy (DMD) in humans, an inherited and progressive disease of striated muscle deterioration that frequently involves pronounced cardiomyopathy(1). Heart failure is the second leading cause of fatalities in DMD1,2. Progress towards defining the molecular basis of disease in DMD has mostly come from studies on skeletal muscle, with comparatively little attention directed to cardiac muscle. The pathophysiological mechanisms involved in cardiac myocytes may differ significantly from skeletal myofibres; this is underscored by the presence of significant cardiac disease in patients with truncated or reduced levels of dystrophin but without skeletal muscle disease(3). Here we show that intact, isolated dystrophin-deficient cardiac myocytes have reduced compliance and increased susceptibility to stretch-mediated calcium overload, leading to cell contracture and death, and that application of the membrane sealant poloxamer 188 corrects these defects in vitro. In vivo administration of poloxamer 188 to dystrophic mice instantly improved ventricular geometry and blocked the development of acute cardiac failure during a dobutamine-mediated stress protocol. Once issues relating to optimal dosing and long-term effects of poloxamer 188 in humans have been resolved, chemical-based membrane sealants could represent a new therapeutic approach for preventing or reversing the progression of cardiomyopathy and heart failure in muscular dystrophy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62706/1/nature03844.pd

Reconstruction of bacterial transcription-coupled repair at single-molecule resolution

International audienc

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Beyond a phenomenological description of magnetostriction

We use ultrafast x-ray and electron diffraction to disentangle spin-lattice coupling of granular FePt in the time domain. The reduced dimensionality of single-crystalline FePt nanoparticles leads to strong coupling of magnetic order and a highly anisotropic three-dimensional lattice motion characterized by a- and b-axis expansion and c-axis contraction. The resulting increase of the FePt lattice tetragonality, the key quantity determining the energy barrier between opposite FePt magnetization orientations, persists for tens of picoseconds. These results suggest a novel approach to laser-assisted magnetic switching in future data storage applications.Comment: 12 pages, 4 figure

Innovation and growth in the UK pharmaceuticals: the case of product and marketing introductions

New drug introductions are key to growth for pharmaceutical firms. However, not all innovations are the same and they may have differential effects that vary by firm size. We use quarterly sales data on UK pharmaceuticals in a dynamic panel model to estimate the impact of product (new drugs) and marketing (additional pack varieties) innovations within a therapeutic class on a firm’s business unit growth. We find that product innovations lead to substantial growth in both the short and long run, whereas a new pack variety only produces short-term effects. The strategies are substitutes but the marginal effects are larger for product innovations relative to additional packs, and the effects are larger for smaller business units. Nonetheless, pack introductions offer a viable short-term growth strategy, especially for small- and medium-sized businesses

The CD34-Related Molecule Podocalyxin Is a Potent Inducer of Microvillus Formation

BACKGROUND: Podocalyxin is a CD34-related transmembrane protein involved in hematopoietic cell homing, kidney morphogenesis, breast cancer progression, and epithelial cell polarization. Although this sialomucin has been shown to block cell adhesion, the mechanisms involved remain enigmatic. It has, however, been postulated that the adaptor proteins NHERF-1 and 2 could regulate apical targeting of Podocalyxin by linking it to the actin cytoskeleton. PRINCIPAL FINDINGS: Here, in contrast, we find that full-length Podocalyxin acts to recruit NHERF-1 to the apical domain. Moreover, we show that ectopic expression of Podocalyxin in epithelial cells leads to microvillus formation along an expanded apical domain that extends laterally to the junctional complexes. Removal of the C-terminal PDZ-binding domain of Podocalyxin abolishes NHERF-1 recruitment but, surprisingly, has no effect on the formation of microvilli. Instead, we find that the extracellular domain and transmembrane region of Podocalyxin are sufficient to direct recruitment of filamentous actin and ezrin to the plasma membrane and induce microvillus formation. CONCLUSIONS/SIGNIFICANCE: Our data suggest that this single molecule can modulate NHERF localization and, independently, act as a key orchestrator of apical cell morphology, thereby lending mechanistic insights into its multiple roles as a polarity regulator, tumor progression marker, and anti-adhesin

The influence of nativity and neighborhoods on breast cancer stage at diagnosis and survival among California Hispanic women

<p>Abstract</p> <p>Background</p> <p>In the US, foreign-born Hispanics tend to live in socioeconomic conditions typically associated with later stage of breast cancer diagnosis, yet they have lower breast cancer mortality rates than their US-born counterparts. We evaluated the impact of nativity (US- versus foreign-born), neighborhood socioeconomic status (SES) and Hispanic enclave (neighborhoods with high proportions of Hispanics or Hispanic immigrants) on breast cancer stage at diagnosis and survival among Hispanics.</p> <p>Methods</p> <p>We studied 37,695 Hispanic women diagnosed from 1988 to 2005 with invasive breast cancer from the California Cancer Registry. Nativity was based on registry data or, if missing, imputed from case Social Security number. Neighborhood variables were developed from Census data. Stage at diagnosis was analyzed with logistic regression, and survival, based on vital status determined through 2007, was analyzed with Cox proportional hazards regression.</p> <p>Results</p> <p>Compared to US-born Hispanics, foreign-born Hispanics were more likely to be diagnosed at an advanced stage of breast cancer (adjusted odds ratio (OR) = 1.14, 95% confidence interval (CI): 1.09-1.20), but they had a somewhat lower risk of breast cancer specific death (adjusted hazard ratio (HR) = 0.94, 95% CI: 0.90-0.99). Living in low SES and high enclave neighborhoods was associated with advanced stage of diagnosis, while living in a lower SES neighborhood, but not Hispanic enclave, was associated with worse survival.</p> <p>Conclusion</p> <p>Identifying the modifiable factors that facilitate this survival advantage in Hispanic immigrants could help to inform specific interventions to improve survival in this growing population.</p