Guidelines for the functional annotation of microRNAs using the Gene Ontology

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual)

Inelastic Light Scattering From Correlated Electrons

Inelastic light scattering is an intensively used tool in the study of electronic properties of solids. Triggered by the discovery of high temperature superconductivity in the cuprates and by new developments in instrumentation, light scattering both in the visible (Raman effect) and the X-ray part of the electromagnetic spectrum has become a method complementary to optical (infrared) spectroscopy while providing additional and relevant information. The main purpose of the review is to position Raman scattering with regard to single-particle methods like angle-resolved photoemission spectroscopy (ARPES), and other transport and thermodynamic measurements in correlated materials. Particular focus will be placed on photon polarizations and the role of symmetry to elucidate the dynamics of electrons in different regions of the Brillouin zone. This advantage over conventional transport (usually measuring averaged properties) indeed provides new insights into anisotropic and complex many-body behavior of electrons in various systems. We review recent developments in the theory of electronic Raman scattering in correlated systems and experimental results in paradigmatic materials such as the A15 superconductors, magnetic and paramagnetic insulators, compounds with competing orders, as well as the cuprates with high superconducting transition temperatures. We present an overview of the manifestations of complexity in the Raman response due to the impact of correlations and developing competing orders. In a variety of materials we discuss which observations may be understood and summarize important open questions that pave the way to a detailed understanding of correlated electron systems.Comment: 62 pages, 48 figures, to appear in Rev. Mod. Phys. High-resolution pdf file available at http://onceler.uwaterloo.ca/~tpd/RMP.pd

Observing Long Colour Flux Tubes in SU(2) Lattice Gauge Theory

We present results of a high statistics study of the chromo field distribution between static quarks in SU(2) gauge theory on lattices of volumes 16^4, 32^4, and 48^3*64, with physical extent ranging from 1.3 fm up to 2.7 fm at beta=2.5, beta=2.635, and beta=2.74. We establish string formation over physical distances as large as 2 fm. The results are tested against Michael's sum rules. A detailed investigation of the transverse action and energy flux tube profiles is provided. As a by-product, we obtain the static lattice potential in unpreceded accuracy.Comment: 66 pages, 29 figures, uuencoded latex file with epsfigures (450 K), supplementary full colour figures are available via ftp, CERN-TH.7413/94 (extended version

Storytelling in Amy Tan’s The bonesetter’s daughter: belonging and the transnationality of home in older age

Amy Tan’s The Bonesetter’s Daughter is a fictional account of a Chinese American woman and her mother, a first generation migrant, who is negotiating dementia in later life. Analysis of diasporic novels can provide insight into migrant belonging, especially the emotional geographies of home and emotional subjectivities of ageing that are not commonly or easily elucidated even by qualitative interviewing methods. This article examines Tan’s construction of ageing as an intergenerational, cultural and emotional process, and highlights the role of storytelling as an everyday home-making practice through which the transnationality of home in older age becomes evident

The Heavy Hadron Spectrum

I discuss the spectrum of hadrons containing heavy quarks ($b$ or $c$), and how well the experimental results are matched by theoretical ideas. Useful insights come from potential models and applications of Heavy Quark Symmetry and these can be compared with new numerical results from the ab initio methods of Lattice QCD.Comment: 64 pages, Latex, lectures at Schladming Winter School 199

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

Young hands, old books: : Drawings by children in a fourteenth-century manuscript, LJS MS. 361

This article scrutinises three marginal drawings in LJS 361, Kislak Center for Special Collections, Rare Books and Manuscripts, University of Pennsylvania Libraries. It first considers the provenance of the manuscript, questioning how it got into the hands of children. Then, it combines developmental psychology with close examination of the material evidence to develop a list of criteria to attribute the drawings to children. There is consideration of the features that help us estimate the age of the artists, and which indicate that one drawing was a collaborative effort between two children. A potential relationship is identified between the doodles and the subject matter of the text, prompting questions about pre-modern child education and literacy. Finally, the article considers the implications of this finding in both codicology and social history since these marginal illustrations demonstrate that children were active in the material life of medieval books

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role

Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells

Plant retinoblastoma-related (RBR) proteins are primarily considered as key regulators of G1/S phase transition, with functional roles in a variety of cellular events during plant growth and organ development. Polyclonal antibody against the C-terminal region of the Arabidopsis RBR1 protein also specifically recognizes the alfalfa 115 kDa MsRBR protein, as shown by the antigen competition assay. The MsRBR protein was detected in all cell cycle phases, with a moderate increase in samples representing G2/M cells. Antibody against the human phospho-pRb peptide (Ser807/811) cross-reacted with the same 115 kDa MsRBR protein and with the in vitro phosphorylated MsRBR protein C-terminal fragment. Phospho-MsRBR protein was low in G1 cells. Its amount increased upon entry into the S phase and remained high during the G2/M phases. Roscovitine treatment abolished the activity of alfalfa MsCDKA1;1 and MsCDKB2;1, and the phospho-MsRBR protein level was significantly decreased in the treated cells. Colchicine block increased the detected levels of both forms of MsRBR protein. Reduced levels of the MsRBR protein in cells at stationary phase or grown in hormone-free medium can be a sign of the division-dependent presence of plant RBR proteins. Immunolocalization of the phospho-MsRBR protein indicated spots of variable number and size in the labelled interphase nuclei and high signal intensity of nuclear granules in prophase. Structures similar to phospho-MsRBR proteins cannot be recognized in later mitotic phases. Based on the presented western blot and immunolocalization data, the possible involvement of RBR proteins in G2/M phase regulation in plant cells is discussed