Structural analysis of the GH43 enzyme Xsa43E from Butyrivibrio proteoclasticus

The rumen of dairy cattle can be thought of as a large, stable fermentation vat and as such it houses a large and diverse community of microorganisms. The bacterium Butyrivibrio proteoclasticus is a representative of a significant component of this microbial community. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fibre-degrading enzymes. This suite of enzymes is essential for the organism to utilize the plant material within the rumen as a fuel source, facilitating its survival in this competitive environment. Xsa43E, a GH43 enzyme from B. proteoclasticus, has been structurally and functionally characterized. Here, the structure of selenomethionine-derived Xsa43E determined to 1.3 Å resolution using single-wavelength anomalous diffraction is reported. Xsa43E possesses the characteristic five-bladed β-propeller domain seen in all GH43 enzymes. GH43 enzymes can have a range of functions, and the functional characterization of Xsa43E shows it to be an arabinofuranosidase capable of cleaving arabinose side chains from short segments of xylan. Full functional and structural characterization of xylan-degrading enzymes will aid in creating an enzyme cocktail that can be used to completely degrade plant material into simple sugars. These molecules have a range of applications as starting materials for many industrial processes, including renewable alternatives to fossil fuels

UTOPIA—User-Friendly Tools for Operating Informatics Applications

Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real-time interaction with complex datasets. Many existing tools have poor user interfaces and limited real-time performance when applied to realistically large datasets; much of the user's cognitive capacity is therefore focused on controlling the tool rather than on performing the research. The UTOPIA project is addressing some of these issues by building reusable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high-performance rendering, and distributed systems is being guided by bioinformaticians and end-user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end-user and application-developer requirements

The PRINTS database: a fine-grained protein sequence annotation and analysis resource—its status in 2012

The PRINTS database, now in its 21st year, houses a collection of diagnostic protein family ‘fingerprints’. Fingerprints are groups of conserved motifs, evident in multiple sequence alignments, whose unique inter-relationships provide distinctive signatures for particular protein families and structural/functional domains. As such, they may be used to assign uncharacterized sequences to known families, and hence to infer tentative functional, structural and/or evolutionary relationships. The February 2012 release (version 42.0) includes 2156 fingerprints, encoding 12 444 individual motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. Here, we report the current status of the database, and introduce a number of recent developments that help both to render a variety of our annotation and analysis tools easier to use and to make them more widely available

Ammonia-hyperproducing bacteria from New Zealand ruminants

Pasture-grazed dairy cows, deer, and sheep were tested for the presence of ammonia-hyperproducing (HAP) bacteria in roll tubes containing a medium in which tryptone and Casamino Acids were the sole nitrogen and energy sources. Colonies able to grow on this medium represented 5.2, 1.3, and 11.6% of the total bacterial counts of dairy cows, deer, and sheep, respectively. A total of 14 morphologically distinct colonies were purified and studied further. Restriction fragment length polymorphisms of 16S rRNA genes indicated that all isolates differed from the previously described HAP bacteria,Clostridium aminophilum, Clostridium sticklandii, and Peptostreptococcus anaerobius. Carbon source utilization experiments showed that five isolates (C2, D1, D4, D5, and S1) were unable to use any, or very few, of the carbon sources tested. Biochemical tests and phylogenetic analyses of 16S ribosomal DNA sequences indicated that all isolates were monensin sensitive; that D1 and S1 belonged to the genusPeptostreptococcus, that D4 and D5 belonged to the familyBacteroidaceae, where D4 was similar to Fusobacterium necrophorum; and that C2 was most similar to an unidentified species from the genus Eubacterium. Growth on liquid medium containing tryptone and Casamino Acids as the sole nitrogen and energy source showed that D1, D4, and S1 grew rapidly (specific growth rates of 0.40, 0.35, and 0.29 h−1, respectively), while C2 and D5 were slow growers (0.25 and 0.10 h−1, respectively). Ammonia production rates were highest in D1 and D4, which produced 945.5 and 748.3 nmol/min per mg of protein, respectively. Tests of individual nitrogen sources indicated that D1 and D4 grew best on tryptone, S1 grew equally well on Casamino Acids or tryptone, and C2 and D5 grew poorly on all nitrogen sources. The intact proteins casein and gelatin did not support significant growth of any of the isolates. These isolates extend the diversity of known HAP rumen bacteria and indicate the presence of significant HAP bacterial populations in pasture-grazed New Zealand ruminants

Perceptions Of School By Two Teenage Boys With Asperger Syndrome And Their Mothers: A Qualitative Study

This qualitative study aimed to develop an understanding of the challenges faced by teenage boys with Asperger syndrome and their mothers. A case study approach was used to collect data from two 13-year-old boys who have Asperger syndrome and their mothers in Queensland, Australia. Data were collected through the use of semi¬structured interviews. The words of the boys and their mothers provide a valuable insight into the personal experiences and feelings of the par¬ticipants. An inductive approach to data analysis identified four themes: (1) developmental differences; (2) problems associated with the general characteristics of Asperger syndrome (i.e. communication and social difficulties, restricted range of interests, a need for routine); (3) stress; and (4) 'masquerading'. The first three themes relate strongly to the current literature, but the emergence of masquerading is of particular interest in developing a fuller understanding of the experiences of individuals with Asperger syndrome at school

METIS: multiple extraction techniques for informative sentences

Summary: METIS is a web-based integrated annotation tool. From single query sequences, the PRECIS component allows users to generate structured protein family reports from sets of related Swiss-Prot entries. These reports may then be augmented with pertinent sentences extracted from online biomedical literature via support vector machine and rule-based sentence classification systems. Availability: Contact: [email protected] Supplementary informatio

Utopia documents: linking scholarly literature with research data

Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged

Spatial coherence measurement of a high average power table-top soft X-ray laser

Includes bibliographical references (page 126).An extraordinarily high degree of spatial coherence from a high average power tabletop 46.9 nm laser was observed in two-pinhole interference experiments. Refractive anti-guiding and gain guiding along a capillary discharge-produced plasma column causes a rapid increase of the spatial coherence with amplifier length. Full spatial coherence was approached with a 36 cm long plasma of very high axial uniformity and a length to diameter ratio exceeding 1000: 1

Spatial coherence measurements of a 13.2 nm transient Nickel-like Cadmium soft x-ray laser pumped at grazing incidence

Includes bibliographical references (pages [12872-12873]).The spatial coherence of a 13.2 nm transient collisional Ni-like Cd soft X-ray laser pumped at 23 degrees grazing incidence was measured in a series of Young's double-slit experiments. We observed pronounced fringe visibility variations associated with microstructures in the beam's intensity profile. The transverse coherence length was measured to be about 1/20 of the beam diameter and did not significantly improve with longer plasma columns. The equivalent incoherent source size is determined to be 10 μm and the laser's peak spectral brightness ~ 3 × 1023 photons/sec/mm2/mrad2 within less than 0.01% spectral bandwidth

An active registry for bioinformatics web services

Summary: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks