On the 2:1 Orbital Resonance in the HD 82943 Planetary System

We present an analysis of the HD 82943 planetary system based on a radial velocity data set that combines new measurements obtained with the Keck telescope and the CORALIE measurements published in graphical form. We examine simultaneously the goodness of fit and the dynamical properties of the best-fit double-Keplerian model as a function of the poorly constrained eccentricity and argument of periapse of the outer planet's orbit. The fit with the minimum chi_{nu}^2 is dynamically unstable if the orbits are assumed to be coplanar. However, the minimum is relatively shallow, and there is a wide range of fits outside the minimum with reasonable chi_{nu}^2. For an assumed coplanar inclination i = 30 deg. (sin i = 0.5), only good fits with both of the lowest order, eccentricity-type mean-motion resonance variables at the 2:1 commensurability, theta_1 and theta_2, librating about 0 deg. are stable. For sin i = 1, there are also some good fits with only theta_1 (involving the inner planet's periapse longitude) librating that are stable for at least 10^8 years. The libration semiamplitudes are about 6 deg. for theta_1 and 10 deg. for theta_2 for the stable good fit with the smallest libration amplitudes of both theta_1 and theta_2. We do not find any good fits that are non-resonant and stable. Thus the two planets in the HD 82943 system are almost certainly in 2:1 mean-motion resonance, with at least theta_1 librating, and the observations may even be consistent with small-amplitude librations of both theta_1 and theta_2.Comment: 24 pages, including 10 figures; accepted for publication in Ap

Two new functions in the WormBase Enrichment Suite

Genome-wide experiments routinely generate large amounts of data that can be hard to interpret biologically. A common approach to interpreting these results is to employ enrichment analyses of controlled languages, known as ontologies, that describe various biological parameters such as gene molecular or biological function. In C. elegans, three distinct ontologies, the Gene Ontology (GO), Anatomy Ontology (AO), and the Worm Phenotype Ontology (WPO) are used to annotate gene function, expression and phenotype, respectively (Ashburner et al. 2000; Lee and Sternberg, 2003; Schindelman et al. 2011). Previously, we developed software to test datasets for enrichment of anatomical terms, called the Tissue Enrichment Analysis (TEA) tool (Angeles-Albores and Sternberg, 2016). Using the same hypergeometric statistical method, we extend enrichment testing to include WPO and GO, offering a unified approach to enrichment testing in C. elegans. The WormBase Enrichment Suite can be accessed via a user-friendly interface at http://www.wormbase.org/tools/enrichment/tea/tea.cgi. To validate the tools, we analyzed a previously published extracellular vesicle (EV)-releasing neuron (EVN) signature gene set derived from dissociated ciliated EV neurons (Wang et al. 2015) using WormBase Enrichment Suite based on the WS262 WormBase release. TEA correctly identified the CEM, hook sensillum and IL2 neuron as enriched tissues. The top phenotype associated with the EVN signature was chemosensory behavior. Gene Ontology enrichment analysis showed that cell projection and cell body were the most enriched cellular components in this gene set, followed by the biological processes neuropeptide signaling pathway and vesicle localization further down. The tutorial script used to generate the figure above can be viewed at: https://github.com/dangeles/TissueEnrichmentAnalysis/blob/master/tutorial/Tutorial.ipynb The addition of Gene Enrichment Analysis (GEA) and Phenotype Enrichment Analysis (PEA) to WormBase marks an important step towards a unified set of analyses that can help researchers to understand genomic datasets. These enrichment analyses will allow the community to fully benefit from the data curation ongoing at WormBase

Commensurate antiferromagnetic ordering in Ba(Fe{1-x}Co{x})2As2 determined by x-ray resonant magnetic scattering at the Fe K-edge

We describe x-ray resonant magnetic diffraction measurements at the Fe K-edge of both the parent BaFe2As2 and superconducting Ba(Fe0.953Co0.047)2As2 compounds. From these high-resolution measurements we conclude that the magnetic structure is commensurate for both compositions. The energy spectrum of the resonant scattering is in reasonable agreement with theoretical calculations using the full-potential linear augmented plane wave method with a local density functional.Comment: 5 pages, 3 figures; accepted for publication in Phys. Rev. B Rapid Com

Tissue enrichment analysis for C. elegans genomics

Background: Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information. Results: We have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans. Conclusions: Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python’s standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results

Fasting induces ketoacidosis and hypothermia in PDHK2/PDHK4-double-knockout mice

The importance of PDHK (pyruvate dehydrogenase kinase) 2 and 4 in regulation of the PDH complex (pyruvate dehydrogenase complex) was assessed in single- and double-knockout mice. PDHK2 deficiency caused higher PDH complex activity and lower blood glucose levels in the fed, but not the fasted, state. PDHK4 deficiency caused similar effects, but only after fasting. Double deficiency intensified these effects in both the fed and fasted states. PDHK2 deficiency had no effect on glucose tolerance, PDHK4 deficiency produced only a modest effect, but double deficiency caused a marked improvement and also induced lower insulin levels and increased insulin sensitivity. In spite of these beneficial effects, the double-knockout mice were more sensitive than wild-type and single-knockout mice to long-term fasting, succumbing to hypoglycaemia, ketoacidosis and hypothermia. Stable isotope flux analysis indicated that hypoglycaemia was due to a reduced rate of gluconeogenesis and that slightly more glucose was converted into ketone bodies in the double-knockout mice. The findings establish that PDHK2 is more important in the fed state, PDHK4 is more important in the fasted state, and survival during long-term fasting depends upon regulation of the PDH complex by both PDHK2 and PDHK4