Library Impact Practice Brief: Supporting Bibliometric Data Needs at Academic Institutions.

This practice brief presents research conducted by staff at the University of Waterloo Library as part of the library’s participation in ARL’s Research Library Impact Framework initiative. The research addressed the question, “How can research libraries support their campus community in accessing needed bibliometric data for institutional-level purposes?” The brief explores: service background, partners, service providers and users, how bibliometric data are used, data sources, key lessons learned, and recommended resource

On religion and cultural policy: notes on the Roman Catholic Church

This paper argues that religious institutions have largely been neglected within the study of cultural policy. This is attributed to the inherently secular tendency of most modern social sciences. Despite the predominance of the ‘secularisation paradigm’, the paper notes that religion continues to promote powerful attachments and denunciations. Arguments between the ‘new atheists’, in particular, Richard Dawkins, and their opponents are discussed, as is Habermas’s conciliatory encounter with Joseph Ratzinger (later Pope Benedict XVI). The paper then moves to a consideration of the Roman Catholic Church as an agent of cultural policy, whose overriding aim is the promotion of ‘Christian consciousness’. Discussion focuses on the contested meanings of this, with reference to (1) the deliberations of Vatican II and (2) the exercise of theological and cultural authority by the Pope and the Congregation for the Doctrine of the Faith (CDF). It is argued that these doctrinal disputes intersect with secular notions of social and cultural policy and warrant attention outside the specialist realm of theological discourse

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems

CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43050/1/10858_2005_Article_4079.pd

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Hardware considerations for preclinical magnetic resonance of the kidney

Magnetic resonance imaging (MRI) is a noninvasive imaging technology that offers unparalleled anatomical and functional detail, along with diagnostic sensitivity. MRI is suitable for longitudinal studies due to the lack of exposure to ionizing radiation. Before undertaking preclinical MRI investigations of the kidney, the appropriate MRI hardware should be carefully chosen to balance the competing demands of image quality, spatial resolution, and imaging speed, tailored to the specific scientific objectives of the investigation. Here we describe the equipment needed to perform renal MRI in rodents, with the aim to guide the appropriate hardware selection to meet the needs of renal MRI applications.This publication is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This chapter on hardware considerations for renal MRI in small animals is complemented by two separate publications describing the experimental procedure and data analysis

Disorder-to-order transition of the active site of human class Pi glutathione transferase, GST P1-1.

Glutathione transferases comprise a large family of cellular detoxification enzymes that function by catalyzing the conjugation of glutathione (GSH) to electron-deficient centers on carcinogens and other toxins. NMR methods have been used to characterize the structure and dynamics of a human class pi enzyme, GST P1-1, in solution. Resonance assignments have been obtained for the unliganded enzyme and the GSH and S-hexylglutathione (GS-hexyl) complexes. Differences in chemical shifts between the GSH and GS-hexyl complexes suggest more extensive structural differences between these two enzyme-ligand complexes than detected by previous crystallographic methods. The NMR studies reported here clearly show that an alpha-helix (alpha2) within the GSH binding site exists in multiple conformations at physiological temperatures in the absence of ligand. A single conformation of alpha2 is induced by the presence of either GSH or GS-hexyl or a reduction in temperature to below 290 K. The large enthalpy of the transition ( approximately 150 kJ/mol) suggests a considerable structural rearrangement of the protein. The Gibbs free energy for the transition to the unfolded form is on the order of -4 to -6 kJ/mol at physiological temperatures (37 degrees C). This order-to-disorder transition contributes substantially to the overall thermodynamics of ligand binding and should be considered in the design of selective inhibitors of class pi glutathione transferases.</p

Data requirements for reliable chemical shift assignments in deuterated proteins.

The information required for chemical shift assignments in large deuterated proteins was investigated using a Monte Carlo approach (Hitchens et al., 2002). In particular, the consequences of missing amide resonances on the reliability of assignments derived from C alpha and CO or from C alpha and C beta chemical shifts was investigated. Missing amide resonances reduce both the number of correct assignments as well as the confidence in these assignments. More significantly, a number of undetectable errors can arise when as few as 9% of the amide resonances are missing from the spectra. However, the use of information from residue specific labeling as well as local and long-range distance constraints improves the reliability and extent of assignment. It is also shown that missing residues have only a minor effect on the assignment of protein-ligand complexes using C alpha and CO chemical shifts and C alpha inter-residue connectivity, provided that the known chemical shifts of the unliganded protein are utilized in the assignment process.</p