Fission stories: using PomBase to understand Schizosaccharomyces pombe biology

PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualization, PomBase also drives innovation in the MOD community

Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences. We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe , and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins' biological roles

FYPO: the fission yeast phenotype ontology.

MOTIVATION: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. RESULTS: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. AVAILABILITY: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/)

PomBase – the scientific resource for fission yeast

The fission yeast Schizosaccharomyces pombe has become well established as a model species for studying conserved cell-level biological processes, especially the mechanics and regulation of cell division. PomBase integrates the S. pombe genome sequence with traditional genetic, molecular and cell biological experimental data as well as the growing body of large datasets generated by emerging high-throughput methods. This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase for infrequent visitors and anyone considering exploring S. pombe in their research

PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information

PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases

White Dwarfs in Globular Clusters: HST Observations of M4

Using WFPC2 on the Hubble Space Telescope, we have isolated a sample of 258 white dwarfs (WDs) in the Galactic globular cluster M4. Fields at three radial distances from the cluster center were observed and sizeable WD populations were found in all three. The location of these WDs in the color-magnitude diagram, their mean mass of 0.51($\pm 0.03$)M$_{\odot}$, and their luminosity function confirm basic tenets of stellar evolution theory and support the results from current WD cooling theory. The WDs are used to extend the cluster main-sequence mass function upward to stars that have already completed their nuclear evolution. The WD/red dwarf binary frequency in M4 is investigated and found to be at most a few percent of all the main-sequence stars. The most ancient WDs found are about 9 Gyr old, a level which is set solely by the photometric limits of our data. Even though this is less than the age of M4, we discuss how these cooling WDs can eventually be used to check the turnoff ages of globular clusters and hence constrain the age of the Universe.Comment: 46 pages, latex, no figures included, figures available at ftp://ftp.astro.ubc.ca/pub/richer/wdfig.uu size 2.7Mb. To be published in the Astrophysical Journa

Photometric constraints on white dwarfs and the identification of extreme objects

It is possible to reliably identify white dwarfs (WDs) without recourse to spectra, instead using photometric and astrometric measurements to distinguish them from Main Sequence stars and quasars. WDs' colours can also be used to infer their intrinsic properties (effective temperature, surface gravity, etc.), but the results obtained must be interpreted with care. The difficulties stem from the existence of a solid angle degeneracy, as revealed by a full exploration of the likelihood, although this can be masked if a simple best-fit approach is used. Conversely, this degeneracy can be broken if a Bayesian approach is adopted, as it is then possible to utilise the prior information on the surface gravities of WDs implied by spectroscopic fitting. The benefits of such an approach are particularly strong when applied to outliers, such as the candidate halo and ultra-cool WDs identified by Vidrih et al. (2007). A reanalysis of these samples confirms their results for the latter sample but suggests that that most of the halo candidates are thick disk WDs in the tails of the photometric noise distribution.Comment: MNRAS in press; 19 pages, 16 figures; major revisions to text but conclusions unchange

Magnetic properties of the S=1/2 quasi-one-dimensional antiferromagnet CaCu2O3

We report single crystal growth and magnetic susceptibility and neutron diffraction studies of the S=1/2 quasi-1D antiferromagnet CaCu2O3. The structure of this material is similar to that of the prototype two-leg spin-ladder compound SrCu2O3. However, the Cu-O-Cu bond angle in the ladder rungs in CaCu2O3 is equal to 123 deg, and therefore the magnetic interaction along the rungs is expected to be much weaker in this material. At high temperatures, the magnetic susceptibility of CaCu2O3 can be decomposed into a contribution from 1D antiferromagnetic chains of finite-size chain segments together with a weak Curie contribution. The intrachain magnetic exchange constant, determined from the magnetic susceptibility measurements, is 2000 K. CaCu2O3 undergoes a Neel transition at T_N=25 K with ordering wavevector of (0.429(5), 0.5, 0.5). The magnetic structure is incommensurate in the direction of the frustrated interchain interaction. Weak commensurate (0.5, 0.5, 0.5) magnetic peaks are also observed below T_N. Application of a magnetic field induces a metamagnetic transition at which the incommensurability of the magnetic structure is substantially reduced. The material possesses only short-range magnetic order above the transition field.Comment: 12 pages, 10 embedded figure

Notes on a paper of Mess

These notes are a companion to the article "Lorentz spacetimes of constant curvature" by Geoffrey Mess, which was first written in 1990 but never published. Mess' paper will appear together with these notes in a forthcoming issue of Geometriae Dedicata.Comment: 26 page

Resonant nonlinear magneto-optical effects in atoms

In this article, we review the history, current status, physical mechanisms, experimental methods, and applications of nonlinear magneto-optical effects in atomic vapors. We begin by describing the pioneering work of Macaluso and Corbino over a century ago on linear magneto-optical effects (in which the properties of the medium do not depend on the light power) in the vicinity of atomic resonances, and contrast these effects with various nonlinear magneto-optical phenomena that have been studied both theoretically and experimentally since the late 1960s. In recent years, the field of nonlinear magneto-optics has experienced a revival of interest that has led to a number of developments, including the observation of ultra-narrow (1-Hz) magneto-optical resonances, applications in sensitive magnetometry, nonlinear magneto-optical tomography, and the possibility of a search for parity- and time-reversal-invariance violation in atoms.Comment: 51 pages, 23 figures, to appear in Rev. Mod. Phys. in Oct. 2002, Figure added, typos corrected, text edited for clarit