Knowledge tree: Putting discourse into computer‐based learning

Most CBL materials currently in use model only the declarative aspects of the learning process. If such courseware is used without careful planning, this can be dangerous because one of the most fundamental aspects of education is the dialogue that occurs between teachers and the students. Traditionally, this has taken place in informal discussions as well as in formal small‐group learning sessions such as the conventional tutorial. However, as the student‐staff ratio increases, so does the opportunity for this type of personal dialogue decrease. Modern networking technology offers a huge potential to add discourse to CBL, but there are many pedagogical problems involved with the intrinsically ephemeral and anarchic nature both of the Internet and of most conferencing or bulletin‐board systems. In this paper we describe a software system called Knowledge Tree (KT) which we have developed to address some of these issues. KT combines a hierarchical concept‐oriented database functionality with that of a Usenet‐style bulletin board Using this, a knowledge garden may be developed for any subject area. These each contain a hypermedia database of frequently asked questions, together with answers provided by subject experts. There is provision for inter‐student discussions of problems and issues. When students ask new questions these are automatically emailed to a relevant subject expert (determined by a subject‐specific concept thesaurus). The answer is then placed in the database which eventually grows to become a valuable teaching resource. KT is discipline‐independent as the concept thesaurus can be changed to encapsulate any domain of knowledge. We have used it in support of conventional lecture courses, as an important component of a multimedia course, and for general IT support. These examples illustrate the role that this system can play both in basic information provision, and in facilitating the discussion of deep issues

SCUBA imaging of NGC 7331 dust ring

We present observations of the spiral galaxy NGC 7331 using the Sub-millimetre Common User Bolometer Array (SCUBA) on the James Clark Maxwell Telescope. We have detected a dust ring of 45 arcsec radius (3.3 kpc) at wavelengths of 450 and 850-micron. The dust ring is in good correspondence with other observations of the ring in the mid-infrared (MIR), CO and radio-continuum, suggesting that the observed dust is associated with the molecular gas and star formation. A B-K colour map shows an analogous ring structure with an asymmetry about the major axis, consistent with the extinction being produced by a dust ring. The derived temperature of the dust lies between 16 and 31 K and the gas-to-dust ratio between 150 and 570, depending on the assumed dust emission efficiency index (beta=1.5 or 2.).Comment: 5 pages, 6 figures, to be published in MNRA

Reliable structural interpretation of small-angle scattering data from bio-molecules in solution - The importance of quality control and a standard reporting framework

Small-angle scattering is becoming an increasingly popular tool for the study of bio-molecular structures in solution. The large number of publications with 3D-structural models generated from small-angle solution scattering data has led to a growing consensus for the need to establish a standard reporting framework for their publication. The International Union of Crystallography recently established a set of guidelines for the necessary information required for the publication of such structural models. Here we describe the rationale for these guidelines and the importance of standardising the way in which small-angle scattering data from bio-molecules and associated structural interpretations are reported. © 2012 Jacques et al.; licensee BioMed Central Ltd

Biological neutron scattering: Now and the future

Neutrons have an important role to play in structural biology. Neutron crystallography, small-angle neutron scattering and inelastic neutron scattering techniques can all contribute unique information on biomolecular structures. In particular, solution scattering techniques can give critical information on the conformations an dispositions of the components of complex assemblies under a wide variety of relevant conditions. The power of these methods are demonstrated for examples by protein/DNA complexes, and Ca{sup 2+}- binding proteins complexed with their regulatory targets. In addition, we demonstrate the utility of a new structural approach suing neutron resonance scattering. The impact of biological neutron scattering to date has been constrained principally by the available fluxes at neutron sources and the true potential of these approaches will only be realized with the development of new more powerful neutron sources

Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution

Small-angle scattering is becoming a mainstream technique for structural molecular biology. As such, it is important to establish guidelines for publication that will ensure that there is adequate reporting of the data and its treatment so that reviewers and readers can independently assess the quality of the data and the basis for any interpretations presented. This article presents a set of preliminary guidelines that emerged after consultation with the IUCr Commission on Small-Angle Scattering and other experts in the field and discusses the rationale for their application. At the 2011 Congress of the IUCr in Madrid, the Commission on Journals agreed to adopt these preliminary guidelines for the presentation of biomolecular structures from small-angle scattering data in IUCr publications. Here, these guidelines are outlined and the reasons for standardizing the way in which small-angle scattering data are presented. © 2012 International Union of Crystallography Printed in Singapore - all rights reserved

Submillimeter Imaging of NGC 891 with SHARC

The advent of submillimeter wavelength array cameras operating on large ground-based telescopes is revolutionizing imaging at these wavelengths, enabling high-resolution submillimeter surveys of dust emission in star-forming regions and galaxies. Here we present a recent 350 micron image of the edge-on galaxy NGC 891, which was obtained with the Submillimeter High Angular Resolution Camera (SHARC) at the Caltech Submillimeter Observatory (CSO). We find that high resolution submillimeter data is a vital complement to shorter wavelength satellite data, which enables a reliable separation of the cold dust component seen at millimeter wavelengths from the warmer component which dominates the far-infrared (FIR) luminosity.Comment: 4 pages LaTeX, 2 EPS figures, with PASPconf.sty; to appear in "Astrophysics with Infrared Surveys: A Prelude to SIRTF

200-µm ISO observations of NGC 6946: evidence for an extended distribution of cold dust

We have used the Infrared Space Observatory (ISO) to obtain a resolved 200-μm image of the nearby spiral galaxy NGC 6946. We compare these observations with those made at 60 and 100 μm by the Infrared Astronomical Satellite (IRAS). Whereas IRAS mainly detected warm dust (T ≈30 K) heated by star-forming regions, ISO detects an extended distribution of cold dust (T ≤ 22 K) that is heated by the general interstellar radiation field. The IRAS emission tends to follow the molecular gas while it appears that the colder dust has a stronger association with atomic hydrogen. The cold dust is more extended in the radial direction than the optical, near-infrared, IRAS and radio continuum (20 cm) emission. The total gas-to-dust mass ratio is found to be ≈290. This is much closer to the Galactic value of ≈160 than the value of 1240 found using IRAS data onl

Near-infrared reddening of extra-galactic GMCs in a face-on geometry

[Abridged] We describe the near-infrared reddening signature of giant molecular clouds (GMCs) in external galaxies. In particular, we examine the E(J-H) and E(H-K) color-excesses, and the effective extinction law observed in discrete GMC regions. We also study the effect of the relative scale height of the GMC distribution to the color-excesses, and to the observed mass function of GMCs. We perform Monte Carlo radiative transfer simulations with 3D models of stellar radiation and clumpy dust distributions, resembling a face-on geometry. The scattered light is included in the models, and near-infrared color maps are calculated from the simulated data. The effective near-infrared reddening law, i.e. the ratio E(J-H)/E(H-K), has a value close to unity in GMC regions. The ratio depends on the relative scale height of GMCs, xi, and for xi values 0.1...0.75 we find the typical ratios of 0.6...1.1. The effective extinction law turns out to be very flat in GMC regions. We find the ratios of apparent extinctions of A(H)/A(K)=1.35...1.55 and A(J)/A(H)=1.15. The effect of the scattered flux on the effective reddening law, as well as on the effective extinction law, is significant. Regarding the GMC mass function, we find no correlation between the input and observed slopes of the mass functions. Rather, the observed slope reflects the parameter $\xi$ and the dynamical range of the mass function. We estimate that only a fraction of 10...20 % of the total mass of GMCs is recovered, if the observed color-excess values are transformed to masses using the Galactic reddening law. In the case of individual clouds the fraction can vary between ~0...50 %.Comment: 8 pages, 10 figures, accepted for publication in A&A. Added missing histograms in Fig.

Calmodulin Binds a Highly Extended HIV-1 MA Protein That Refolds Upon Its Release

Calmodulin (CaM) expression is upregulated upon HIV-1 infection and interacts with proteins involved in viral processing, including the multifunctional HIV-1 MA protein. We present here the results of studies utilizing small-angle neutron scattering with contrast variation that, when considered in the light of earlier fluorescence and NMR data, show CaM binds MA in an extended open-clamp conformation via interactions with two tryptophans that are widely spaced in sequence and space. The interaction requires a disruption of the MA tertiary fold such that MA becomes highly extended in a long snakelike conformation. The CaM-MA interface is extensive, covering ∼70% of the length of the MA such that regions known to be important in MA interactions with critical binding partners would be impacted. The CaM conformation is semiextended and as such is distinct from the classical CaM-collapse about short α-helical targets. NMR data show that upon dissociation of the CaM-MA complex, either by the removal of Ca2+ or increasing ionic strength, MA reforms its native tertiary contacts. Thus, we observe a high level of structural plasticity in MA that may facilitate regulation of its activities via intracellular Ca2+-signaling during viral processing. © 2012 Biophysical Society

The structure of TTHA0988 from Thermus thermophilus, a KipI-KipA homologue incorrectly annotated as allophanate hydrolase

The Thermus thermophilus protein TTHA0988 is a protein of unknown function which represents a fusion of two proteins found almost ubiquitously across the bacterial kingdom. These two proteins perform a role regulating sporulation in Bacillus subtilis, where they are known as KipI and KipA. kipI and kipA genes are usually found immediately adjacent to each other and are often fused to produce a single polypeptide, as is the case with TTHA0988. Here, three crystal forms are reported of TTHA0988, the first structure to be solved from the family of `KipI-KipA fusion' proteins. Comparison of the three forms reveals structural flexibility which can be described as a hinge motion between the `KipI' and `KipA' components. TTHA0988 is annotated in various databases as a putative allophanate hydrolase. However, no such activity could be identified and genetic analysis across species with known allophanate hydrolases indicates that a misannotation has occurred. © 2011, Wiley-Blackwell. The definitive version is available at www3.interscience.wiley.co