Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis

Xylanases (EC 3.2.1.8 endo-1,4-glycosyl hydrolase) catalyze the hydrolysis of xylan, an abundant hemicellulose of plant cell walls. Access to the catalytic site of GH11 xylanases is regulated by movement of a short beta-hairpin, the so-called thumb region, which can adopt open or closed conformations. A crystallographic study has shown that the D11F/R122D mutant of the GH11 xylanase A from Bacillus subtilis (BsXA) displays a stable "open" conformation, and here we report a molecular dynamics simulation study comparing this mutant with the native enzyme over a range of temperatures. The mutant open conformation was stable at 300 and 328 K, however it showed a transition to the closed state at 338 K. Analysis of dihedral angles identified thumb region residues Y113 and T123 as key hinge points which determine the open-closed transition at 338 K. Although the D11F/R122D mutations result in a reduction in local inter-intramolecular hydrogen bonding, the global energies of the open and closed conformations in the native enzyme are equivalent, suggesting that the two conformations are equally accessible. These results indicate that the thumb region shows a broader degree of energetically permissible conformations which regulate the access to the active site region. The R122D mutation contributes to the stability of the open conformation, but is not essential for thumb dynamics, i.e., the wild type enzyme can also adapt to the open conformation.

Low-dimensional, hinged bar-code metal oxide layers and free-standing, ordered organic nanostructures from turbostratic vanadium oxide

Both low-dimensional bar-coded metal oxide layers, which exhibit molecular hinging, and free-standing organic nanostructures can be obtained from unique nanofibers of vanadium oxide (VOx). The nanofibers are successfully synthesized by a simple chemical route using an ethanolic solution of vanadium pentoxide xerogel and dodecanethiol resulting in a double bilayered laminar turbostratic structure. The formation of vanadium oxide nanofibers is observed after hydrothermal treatment of the thiol-intercalated xerogel, resulting in typical lengths in the range 2–6 µm and widths of about 50–500 nm. We observe concomitant hinging of the flexible nanofiber lamina at periodic hinge points in the final product on both the nanoscale and molecular level. Bar-coded nanofibers comprise alternating segments of organic–inorganic (thiols–VOx) material and are amenable to segmented, localized metal nanoparticle docking. Under certain conditions free-standing bilayered organic nanostructures are realized.

Common depth points and associated geographic coordinates

Fluids in subduction zones can influence seismogenic behaviour and prism morphology. The Eastern Makran subduction zone, offshore Pakistan, has a very thick incoming sediment section of up to 7.5 km, providing a large potential fluid source to the accretionary prism. A hydrate-related bottom simulating reflector (BSR), zones of high amplitude reflectivity, seafloor seep sites and reflective thrust faults are present across the accretionary prism, indicating the presence of fluids and suggesting active fluid migration. High amplitude free gas zones and seep sites are primarily associated with anticlinal hinge traps, and fluids here appear to be sourced from shallow biogenic sources and migrate to the seafloor along minor normal faults. There are no observed seep sites associated with the surface expression of the wedge thrust faults, potentially due to burial of the surface trace by failure of the steep thrust ridge slopes. Thrust fault reflectivity is restricted to the upper 3 km of sediment and the deeper décollement is non-reflective. We interpret that fluids and overpressure are not common in the deeper stratigraphic section. Thermal modelling of sediments at the deformation front suggests that the deeper sediment section is relatively dewatered and not currently contributing to fluid expulsion in the Makran accretionary prism.

Classification with a reject option using a hinge loss

We consider the problem of binary classification where the classifier can, for a particular cost, choose not to classify an observation. Just as in the conventional classification problem, minimization of the sample average of the cost is a difficult optimization problem. As an alternative, we propose the optimization of a certain convex loss function φ, analogous to the hinge loss used in support vector machines (SVMs). Its convexity ensures that the sample average of this surrogate loss can be efficiently minimized. We study its statistical properties. We show that minimizing the expected surrogate loss—the φ-risk—also minimizes the risk. We also study the rate at which the φ-risk approaches its minimum value. We show that fast rates are possible when the conditional probability P(Y=1|X) is unlikely to be close to certain critical values.

Communications and learning structures that facilitate transfer of knowledge at innovation transition points

Innovation processes are rarely smooth and disruptions often occur at transition points were one knowledge domain passes the technology on to another domain. At these transition points communication is a key component in assisting the smooth hand over of technologies. However for smooth transitions to occur we argue that appropriate structures have to be in place and boundary spanning activities need to be facilitated. This paper presents three case studies of innovation processes and the findings support the view that structures and boundary spanning are essential for smooth transitions. We have explained the need to pass primary responsibility between agents to successfully bring an innovation to market. We have also shown the need to combine knowledge through effective communication so that absorptive capacity is built in process throughout the organisation rather than in one or two key individuals.

Points of convergence and divergence : normative, institutional and operational relationships between R2P and POC

As an international norm, the Responsibility to Protect (R2P) has gained substantial influence and institutional presence—and created no small controversy—in the ten years since its first conceptualisation. Conversely, the Protection of Civilians in Armed Conflict (PoC) has a longer pedigree and enjoys a less contested reputation. Yet UN Security Council action in Libya in 2011 has thrown into sharp relief the relationship between the two. UN Security Council Resolutions 1970 and 1973 follow exactly the process envisaged by R2P in response to imminent atrocity crimes, yet the operative paragraphs of the resolutions themselves invoke only PoC. This article argues that, while the agendas of PoC and R2P converge with respect to Security Council action in cases like Libya, outside this narrow context it is important to keep the two norms distinct. Peacekeepers, humanitarian actors, international lawyers, individual states and regional organisations are required to act differently with respect to the separate agendas and contexts covered by R2P and PoC. While overlap between the two does occur in highly visible cases like Libya, neither R2P nor PoC collapses normatively, institutionally or operationally into the other.

The FAM deubiquitylating enzyme localizes to multiple points of protein trafficking in epithelia, where it associates with E-cadherin and β-catenin

Ubiquitylation is a necessary step in the endocytosis and lysosomal trafficking of many plasma membrane proteins and can also influence protein trafficking in the biosynthetic pathway. Although a molecular understanding of ubiquitylation in these processes is beginning to emerge, very little is known about the role deubiquitylation may play. Fat Facets in mouse (FAM) is substrate-specific deubiquitylating enzyme highly expressed in epithelia where it interacts with its substrate, β-catenin. Here we show, in the polarized intestinal epithelial cell line T84, FAM localized to multiple points of protein trafficking. FAM interacted with β-catenin and E-cadherin in T84 cells but only in subconfluent cultures. FAM extensively colocalized with β-catenin in cytoplasmic puncta but not at sites of cell-cell contact as well as immunoprecipitating with β-catenin and E-cadherin from a higher molecular weight complex (~500 kDa). At confluence FAM neither colocalized with, nor immunoprecipitated, β-catenin or E-cadherin, which were predominantly in a larger molecular weight complex (~2 MDa) at the cell surface. Overexpression of FAM in MCF-7 epithelial cells resulted in increased β-catenin levels, which localized to the plasma membrane. Expression of E-cadherin in L-cell fibroblasts resulted in the relocalization of FAM from the Golgi to cytoplasmic puncta. These data strongly suggest that FAM associates with E-cadherin and β-catenin during trafficking to the plasma membrane.

Compass points : the locations, landscapes and coordinates of identities in contemporary performance making : proceedings of the Australasian Association for Theatre, Drama & Performance Studies (ADSA) Conference 2012

Compass Points: The Locations, Landscapes and Coordinates of Identities' the Australasian Association for Theatre, Drama and Performance Studies (ADSA) Conference 2012 was held at Queensland University of Technology, July 3-6 2012. The Conference was sponsored by the Australasian Association for Theatre, Drama and Performance Studies (ADSA), Queensland University of Technology (QUT), Ian Potter Foundation, Arts Queensland, La Boite Theatre Company and Queensland Theatre Company. The papers selected for this collection represent a small sample of the scope, depth and diversity of scholarship presented at the conference - they cover a range of genres, cultures and contexts in contemporary performance making from autobiography, to playwrighting, to public space performance and beyond. The papers collected have been peer-reviewed to Australia’s Department of Education, Science and Training (DEST) standards - each has been subject to two blind reviews, followed by acceptance, rejection or revision, and editing of accepted papers - by colleagues from Australasia and overseas. The review process for the conference publication was separate from the review process for acceptance of abstracts for the actual conference presentations. The conference convenors, Bree Hadley and Caroline Heim, edited the collection, and would like to thank all those who gave their time to advise on the peer review process and act as reviewers - Tom Burvill, Christine Comans, Sean Edgecomb, Angela Campbell, Natalie Lazaroo, Jo Loth, Meg Mumford, Ulrike Garde, Laura Ginters, Andre Bastian, Sam Trubridge, Delyse Ryan, Georgia Seffrin, Gillian Arrighi, Rand Hazou, Rob Pensalfini, Sue Fenty-Studham, Mark Radvan, Rob Conkie, Kris Plummer, Lisa Warrington, Kate Flaherty, Bryoni Tresize, Janys Hayes, Lisa Warrington, Teresa Izzard, Kim Durban, Veronica Kelly, Adrian Keirnander, James Davenport, Julie Robson and others. We, and the authors, appreciate the rigour and care with which peers have approached the scholarship presented here. This collection was published in final form on July 3rd 2012, the first day of the ADSA Conference 2012.

Green Star points obtained by Australian building projects

The green building trend has increased rapidly worldwide in recent decades as a means of addressing growing concerns over climate change and global warming and to reduce the impact of the building industry on the environment. A significant contribution in Australia is the use of a series of rating tools by the Green Building Council Australia (GBCA) for the certification of various types of buildings. This paper reviews the use of the Green Star system in Australian building construction, and investigates the potential challenges involved in acquiring the certification of Australian buildings by critically analysing a database of most recently certified GBCA projects. The results show that management-related credits and innovation-related credits are the easiest and most difficult respectively to obtain. Additionally, 6-Star green buildings achieve significantly higher points than other certified buildings in the Energy category. In contrast, 4 Star green buildings achieve more points in the Material category than 5 and 6 Star buildings. The study offers a useful reference for both property developers and project teams to obtain a better understanding of the rating scheme and consequently the effective preparation of certification documentation.

Refined plastic hinge analysis of steel frame structures comprising non-compact sections : II : verification

Application of "advanced analysis" methods suitable for non-linear analysis and design of steel frame structures permits direct and accurate determination of ultimate system strengths, without resort to simplified elastic methods of analysis and semi-empirical specification equations. However, the application of advanced analysis methods has previously been restricted to steel frames comprising only compact sections that are not influenced by the effects of local buckling. A refined plastic hinge method suitable for practical advanced analysis of steel frame structures comprising non-compact sections is presented in a companion paper. The method implicitly accounts for the effects of gradual cross-sectional yielding, longitudinal spread of plasticity, initial geometric imperfections, residual stresses, and local buckling. The accuracy and precision of the method for the analysis of steel frames comprising non-compact sections is established in this paper by comparison with a comprehensive range of analytical benchmark frame solutions. The refined plastic hinge method is shown to be more accurate and precise than the conventional individual member design methods based on elastic analysis and specification equations.