On the Ambiguity of Spontaneously Broken Gauge Symmetry

Local gauge symmetries cannot break spontaneously, according to Elitzur's theorem, but this leaves open the possibility of breaking some global subgroup of the local gauge symmetry, which is typically the gauge symmetry remaining after certain (e.g. Coulomb or Landau) gauge choices. We show that in an SU(2) gauge-Higgs system such symmetries do indeed break spontaneously, but the location of the breaking in the phase diagram depends on the choice of global subgroup. The implication is that there is no unique broken gauge symmetry, but rather many symmetries which break in different places. The problem is to decide which, if any, of these gauge symmetry breakings is associated with a transition between physically different, confining and non-confining phases. Several proposals - Kugo-Ojima, Coulomb, and monopole condensate - are discussed.Comment: 9 pages, 6 figures. v2: references adde

Phase diagram of the lattice SU(2) Higgs model

We perform a detailed study of the phase diagram of the lattice Higgs SU(2) model with fixed Higgs field length. Consistently with previsions based on the Fradkin Shenker theorem we find a first order transition line with an endpoint whose position we determined. The diagram also shows cross-over lines: the cross-over corresponding to the pure SU(2) bulk is also present at nonzero coupling with the Higgs field and merges with the one that continues the line of first order transition beyond the critical endpoint. At high temperature the first order line becomes a crossover, whose position moves by varying the temperature.Comment: 18 pages, 15 figure

The Generic Genome Browser: A building block for a model organism system database

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org

A genetic screen for components of the mammalian RNA interference pathway in Bloom-deficient mouse embryonic stem cells

Genetic screens performed in model organisms have helped identify key components of the RNA interference (RNAi) pathway. Recessive genetic screens have recently become feasible through the use of mouse embryonic stem (ES) cells that are Bloom's syndrome protein (Blm) deficient. Here, we developed and performed a recessive genetic screen to identify components of the mammalian RNAi pathway in Blm-deficient ES cells. Genome-wide mutagenesis using a retroviral gene trap strategy resulted in the isolation of putative homozygous RNAi mutant cells. Candidate clones were confirmed by an independent RNAi-based reporter assay and the causative gene trap integration site was identified using molecular techniques. Our screen identified multiple mutant cell lines of Argonaute 2 (Ago2), a known essential component of the RNAi pathway. This result demonstrates that true RNAi components can be isolated by this screening strategy. Furthermore, Ago2 homozygous mutant ES cells provide a null genetic background to perform mutational analyses of the Ago2 protein. Using genetic rescue, we resolve an important controversy regarding the role of two phenylalanine residues in Ago2 activity

The Reactome pathway knowledgebase

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation

Reactome knowledgebase of human biological pathways and processes

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms

The systematic annotation of the three main GPCR families in Reactome

Reactome is an open-source, freely available database of human biological pathways and processes. A major goal of our work is to provide an integrated view of cellular signalling processes that spans from ligand–receptor interactions to molecular readouts at the level of metabolic and transcriptional events. To this end, we have built the first catalogue of all human G protein-coupled receptors (GPCRs) known to bind endogenous or natural ligands. The UniProt database has records for 797 proteins classified as GPCRs and sorted into families A/1, B/2 and C/3 on the basis of amino accid sequence. To these records we have added details from the IUPHAR database and our own manual curation of relevant literature to create reactions in which 563 GPCRs bind ligands and also interact with specific G-proteins to initiate signalling cascades. We believe the remaining 234 GPCRs are true orphans. The Reactome GPCR pathway can be viewed as a detailed interactive diagram and can be exported in many forms. It provides a template for the orthology-based inference of GPCR reactions for diverse model organism species, and can be overlaid with protein–protein interaction and gene expression datasets to facilitate overrepresentation studies and other forms of pathway analysis

Accessing directly the properties of fundamental scalars in the confinement and Higgs phase

The properties of elementary particles are encoded in their respective propagators and interaction vertices. For a SU(2) gauge theory coupled to a doublet of fundamental complex scalars these propagators are determined in both the Higgs phase and the confinement phase and compared to the Yang-Mills case, using lattice gauge theory. Since the propagators are gauge-dependent, this is done in the Landau limit of 't Hooft gauge, permitting to also determine the ghost propagator. It is found that neither the gauge boson nor the scalar differ qualitatively in the different cases. In particular, the gauge boson acquires a screening mass, and the scalar's screening mass is larger than the renormalized mass. Only the ghost propagator shows a significant change. Furthermore, indications are found that the consequences of the residual non-perturbative gauge freedom due to Gribov copies could be different in the confinement and the Higgs phase.Comment: 11 pages, 6 figures, 1 table; v2: one minor error corrected; v3: one appendix on systematic uncertainties added and some minor changes, version to appear in EPJ

Reactome knowledgebase of human biological pathways and processes

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms

The Protein Ontology: a structured representation of protein forms and complexes

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontology Foundry