Why one-kilobase sequences from mitochondrial DNA fail to solve the Hoatzin phylogenetic enigma.

To address the suitability of mitochondrial DNA sequence data for higher avian systematics, cytochrome b sequences for nine species of Cuculiformes and Galliformes were gathered and compared to those of the Hoatzin, a specialized bird whose phylogenetic affinities have long puzzled ornithologists. Additional avian cytochrome b sequences from GenBank also were incorporated into the comparisons. Various phenetic and parsimony analyses applied to the molecular data coded in four formats (nucleotide sequences, purines versus pyrimidines, first and second positions of codons, and translated amino acid sequences) yielded several consistent phylogenetic arrangements, including the distinction of Galliformes from Cuculiformes, a clade composed of the Guira Cuckoo and Groove-billed Ani (Crotophagidae) to the exclusion of the other assayed cuculiforms (Cuculidae and Coccyzidae), and a clade composed of the New World quail (Odontophoridae, in the Sibley-Ahlquist classification) as a sister group to most or all Old World galliforms assayed (Phasianidae and Numididae). The latter result is of particular interest because it supports a controversial systematic realignment of the Galliformes based on DNA-DNA hybridization data. With regard to the phylogenetic position of the Hoatzin, the analysis differed in face-value outcome, although alternative clades were in all cases poorly supported by bootstrapping, and internodal distances were small relative to the range of genetic separations within either Cuculiformes or Galliformes. These uncertainties in phylogenetic resolution of the Hoatzin appear to be attributable to shallow slopes in the regressions relating cytochrome b sequence differences to evolutionary time, in conjunction with homoplasy in the data, sampling error in the estimation of genetic differences, and the relatively close temporal placements of relevant evolutionary nodes

Decays of metastable vacua in SQCD

The decay rates of metastable SQCD vacua in ISS-type models, both towards supersymmetric vacua as well as towards other nonsupersymmetric configurations arising in theories with elementary spectators, are estimated numerically in the semiclassical approximation by computing the corresponding multifield bounce configurations. The scaling of the bounce action with respect to the most relevant dimensionless couplings and ratios of scales is analyzed. In the case of the decays towards the susy vacua generated by nonperturbative effects, the results confirm previous analytical estimations of this scaling, obtained by assuming a triangular potential barrier. The decay rates towards susy vacua generated by R-symmetry breaking interactions turn out to be more than sufficiently suppressed for the phenomenologically relevant parameter range, and their behavior in this regime differs from analytic estimations valid for parametrically small scale ratios. It is also shown that in models with spectator fields, even though the decays towards vacua involving nonzero spectator VEVs don't have a strong parametric dependence on the scale ratios, the ISS vacuum can still be made long-lived in the presence of R-symmetry breaking interactions.Comment: 22 pages, 7 figure

Holographic metastability

We show how supersymmetric QCD in a slice of AdS can naturally acquire metastable vacua. The formulation closely follows that of Intriligator, Seiberg and Shih (ISS), with an "electric" sector on the UV brane and a "magnetic" sector on the IR brane. However the 't Hooft anomaly matching that constrains the Seiberg duality central to ISS is replaced by anomaly inflow and cancellation, and the source of strong coupling is the CFT to which the theory couples rather than the gauge groups. The theory contains an anomaly free R-symmetry that, when broken by UV effects, leads to an O'Raifeartaigh model on the IR brane. In contrast to ISS, the R-symmetry breaking in the UV can be maximal, and yet the R-symmetry breaking in the IR theory remains under strict control: there is no need for retrofitting of small parameters.Comment: 20 pages, 2 figure

QCD axion and quintessential axion

The axion solution of the strong CP problem is reviewed together with the other strong CP solutions. We also point out the quintessential axion(quintaxion) whose potential can be extremely flat due to the tiny ratio of the hidden sector quark mass and the intermediate hidden sector scale. The quintaxion candidates are supposed to be the string theory axions, the model independent or the model dependent axions.Comment: 15 pages. Talk presented at Castle Ringberg, June 9-14, 200

Quantum Gravity in 2+1 Dimensions: The Case of a Closed Universe

In three spacetime dimensions, general relativity drastically simplifies, becoming a ``topological'' theory with no propagating local degrees of freedom. Nevertheless, many of the difficult conceptual problems of quantizing gravity are still present. In this review, I summarize the rather large body of work that has gone towards quantizing (2+1)-dimensional vacuum gravity in the setting of a spatially closed universe.Comment: 61 pages, draft of review for Living Reviews; comments, criticisms, additions, missing references welcome; v2: minor changes, added reference

Bayesian inference of biochemical kinetic parameters using the linear noise approximation

Background Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the deveopment of effective statistical methods to calibrate such models against available data. Given the prevalence of stochasticity and noise in biochemical systems inference for stochastic models is of special interest. In this paper we present a simple and computationally efficient algorithm for the estimation of biochemical kinetic parameters from gene reporter data. Results We use the linear noise approximation to model biochemical reactions through a stochastic dynamic model which essentially approximates a diffusion model by an ordinary differential equation model with an appropriately defined noise process. An explicit formula for the likelihood function can be derived allowing for computationally efficient parameter estimation. The proposed algorithm is embedded in a Bayesian framework and inference is performed using Markov chain Monte Carlo. Conclusion The major advantage of the method is that in contrast to the more established diffusion approximation based methods the computationally costly methods of data augmentation are not necessary. Our approach also allows for unobserved variables and measurement error. The application of the method to both simulated and experimental data shows that the proposed methodology provides a useful alternative to diffusion approximation based methods

Agent based modelling helps in understanding the rules by which fibroblasts support keratinocyte colony formation

Background: Autologous keratincoytes are routinely expanded using irradiated mouse fibroblasts and bovine serum for clinical use. With growing concerns about the safety of these xenobiotic materials, it is desirable to culture keratinocytes in media without animal derived products. An improved understanding of epithelial/mesenchymal interactions could assist in this. Methodology/Principal Findings: A keratincyte/fibroblast o-culture model was developed by extending an agent-based keratinocyte colony formation model to include the response of keratinocytes to both fibroblasts and serum. The model was validated by comparison of the in virtuo and in vitro multicellular behaviour of keratinocytes and fibroblasts in single and co-culture in Greens medium. To test the robustness of the model, several properties of the fibroblasts were changed to investigate their influence on the multicellular morphogenesis of keratinocyes and fibroblasts. The model was then used to generate hypotheses to explore the interactions of both proliferative and growth arrested fibroblasts with keratinocytes. The key predictions arising from the model which were confirmed by in vitro experiments were that 1) the ratio of fibroblasts to keratinocytes would critically influence keratinocyte colony expansion, 2) this ratio needed to be optimum at the beginning of the co-culture, 3) proliferative fibroblasts would be more effective than irradiated cells in expanding keratinocytes and 4) in the presence of an adequate number of fibroblasts, keratinocyte expansion would be independent of serum. Conclusions: A closely associated computational and biological approach is a powerful tool for understanding complex biological systems such as the interactions between keratinocytes and fibroblasts. The key outcome of this study is the finding that the early addition of a critical ratio of proliferative fibroblasts can give rapid keratinocyte expansion without the use of irradiated mouse fibroblasts and bovine serum

Maternal educational level and risk of gestational hypertension: the Generation R Study.

We examined whether maternal educational level as an indicator of socioeconomic status is associated with gestational hypertension. We also examined the extent to which the effect of education is mediated by maternal substance use (that is smoking, alcohol consumption and illegal drug use), pre-existing diabetes, anthropometrics (that is height and body mass index (BMI)) and blood pressure at enrolment. This was studied in 3262 Dutch pregnant women participating in the Generation R Study, a population-based cohort study. Level of maternal education was established by questionnaire at enrolment, and categorized into high, mid-high, mid-low and low. Diagnosis of gestational hypertension was retrieved from medical records using standard criteria. Odds ratios (OR) of gestational hypertension for educational levels were calculated, adjusted for potential confounders and additionally adjusted for potential mediators. Adjusted for age and gravidity, women with mid-low (OR: 1.52; 95% CI: 1.02, 2.27) and low education (OR: 1.30; 95% CI: 0.80, 2.12) had a higher risk of gestational hypertension than women with high education. Additional adjustment for substance use, pre-existing diabetes, anthropometrics and blood pressure at enrolment attenuated these ORs to 1.09 (95% CI: 0.70, 1.69) and 0.89 (95% CI: 0.50, 1.58), respectively. These attenuations were largely due to the effects of BMI and blood pressure at enrolment. Women with relatively low educational levels have a higher risk of gestational hypertension, which is largely due to higher BMI and blood pressure levels from early pregnancy. The higher risk of gestational hypertension in these women is probably caused by pre-existing hypertensive tendencies that manifested themselves during pregnancy

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