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

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

Further studies on relic neutrino asymmetry generation II: a rigorous treatment of repopulation in the adiabatic limit

We derive an approximate relic neutrino asymmetry evolution equation that systematically incorporates repopulation processes from the full quantum kinetic equations (QKEs). It is shown that in the collision dominant epoch, the said equation reduces precisely to the expression obtained previously from the static/adiabatic approximation. The present treatment thus provides a rigorous justification for the seemingly incongruous assumptions of a negligible repopulation function and instantaneous repopulation sometimes employed in earlier works.Comment: RevTeX, 11 pages, no figure

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

Bilateral symmetry breaking in a nonlinear Fabry-Perot cavity exhibiting optical tristability

We show the existence of a region in the parameter space that defines the field dynamics in a Fabry-Perot cylindrical cavity, where three output stable stationary states of the light are possible for a given localized incident field. Two of these states do not preserve the bilateral (i.e. left-right) symmetry of the entire system. These broken-symmetry states are the high-transmission nonlinear modes of the system. We also discuss how to excite these states.Comment: 5 pages, 5 figure

Transition Region Emission from Solar Flares during the Impulsive Phase

There are relatively few observations of UV emission during the impulsive phases of solar flares, so the nature of that emission is poorly known. Photons produced by solar flares can resonantly scatter off atoms and ions in the corona. Based on off-limb measurements by SOHO/UVCS, we derive the O VI $\lambda$1032 luminosities for 29 flares during the impulsive phase and the Ly$\alpha$ luminosities of 5 flares, and we compare them with X-ray luminosities from GOES measurements. The upper transition region and lower transition region luminosities of the events observed are comparable. They are also comparable to the luminosity of the X-ray emitting gas at the beginning of the flare, but after 10-15 minutes the X-ray luminosity usually dominates. In some cases we can use Doppler dimming to estimate flow speeds of the O VI emitting gas, and 5 events show speeds in the 40 to 80 $\rm km s^{-1}$ range. The O VI emission could originate in gas evaporating to fill the X-ray flare loops, in heated chromospheric gas at the footpoints, or in heated prominence material in the coronal mass ejection. All three sources may contribute in different events or even in a single event, and the relative timing of UV and X-ray brightness peaks, the flow speeds, and the total O VI luminosity favor each source in one or more events.Comment: 18 pages, 8 figures, 3 table

Unconventional ferromagnetic and spin-glass states of the reentrant spin glass Fe0.7Al0.3

Spin excitations of single crystal Fe0.7Al0.3 were investigated over a wide range in energy and reciprocal space with inelastic neutron scattering. In the ferromagnetic phase, propagating spin wave modes become paramagnon-like diffusive modes beyond a critical wave vector q0, indicating substantial disorder in the long-range ordered state. In the spin glass phase, spin dynamics is strongly q-dependent, suggesting remnant short-range spin correlations. Quantitative model for S(energy,q) in the ``ferromagnetic'' phase is determined.Comment: 4 pages, 5 figure

WormBase: a multi-species resource for nematode biology and genomics

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system

Energy-dependent solar neutrino flux depletion in the Exact Parity Model and implications for SNO, SuperKamiokande and BOREXINO

Energy-dependent solar neutrino flux reduction caused by the Mikheyev-Smirnov-Wolfenstein (MSW) effect is applied to the Exact Parity Model. Several scenarios are possible, depending on the region of parameter space chosen. The interplay between intergenerational MSW transitions and vacuum ``intragenerational'' ordinary-mirror neutrino oscillations is discussed. Expectations for the ratio of charged to neutral current event rates at the Sudbury Neutrino Observatory (SNO) are estimated. The implications of the various scenarios for the Boron neutrino energy spectrum and BOREXINO are briefly discussed. The consequences of MSW-induced solar neutrino depletion within the Exact Parity Model differ in interesting ways from the standard $\nu_e - \nu_{\mu, \tau}$ and $\nu_e - \nu_s$ cases. The physical causes of these differences are determined.Comment: 43 pages, 8 figures, RevTeX; to appear in Phys. Rev. D, accepted versio