New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

Examining the effect of exit separation on aircraft evacuation performance during 90-second certification trials using evacuation modelling techniques

This paper examines the influence of exit separation, exit availability and seating configuration on aircraft evacuation efficiency and evacuation time. The purpose of this analysis is to explore how these parameters influence the 60-foot exit separation requirement found in aircraft certification rules. The analysis makes use of the airEXODUS evacuation model and is based on a typical wide-body aircraft cabin section involving two pairs of Type-A exits located at either end of the section with a maximum permissible loading of 220 passengers located between the exits. The analysis reveals that there is a complex relationship between exit separation and evacuation efficiency. A main finding of this work is that for the cabin section examined, with a maximum passenger load of 220 and under certification conditions, exit separations up to 170ft will result in approximately constant total evacuation times and average personal evacuation times. This practical exit separation threshold is decreased to 114ft if another combination of exits is selected. While other factors must also be considered when determining maximum allowable exit separations, these results suggest it is not possible to mandate a maximum exit separation without taking into consideration exit type, exit availability and aircraft configuration.

Issues in second language proficiency

Benati provides clarity about the characteristics and notion of language proficiency in the field of second language acquisition. He looks at four areas of research paradigmatically related to the role of proficiency: theorizing and measuring second language proficiency; the dimensions of L2 proficiency; factors contributing to the attainment of L2 proficiency and attaining L2 proficiency in the classroom. It also contains a variety of research accounts about the specific factors which have an effect on proficiency together with a theorised measurement of proficiency in second language research. It will be required reading for researchers in applied linguistics and second language acquisition.

Key terms in second language acquisition

Key Terms in Second Language Acquisition includes definitions of key terms within second language acquisition, and also provides accessible summaries of the key issues within this complex area of study. The final section presents a list of key readings in second language acquisition that signposts the reader towards classic articles and also provides a springboard to further study.

[Book Review] The role of formal features in second language acquisition - edited by J. Liceras, H. Zobl, and H. Goodluck

Book review of: J. Liceras, H. Zobl, and H. Goodluck (eds.), 2008, The Role of Formal Features in Second Language Acquisition. London/New York: Lawrence Erlbaum Associates, 577 pages, ISBN: 0-8058-5354-5.

Second language processing: an analysis of theory, problems and possible solutions

Second Language Processing examines the problems facing learners in the second language classroom from the theoretical perspectives of Processing Instruction (structured input) and Enhanced Input. These two theories are brought to bear on a variety of processing problems, such as the difficulty of connecting second language grammatical forms encoding tense and mood as well as noun-adjective agreement with their meaning. Empirical studies examine a range of languages including Japanese, Italian and Spanish, through which the authors suggest practical solutions to these processing problems.

Twentieth Century Society Spring lecture series: second lives for Twentieth Century masterpieces

The Twentieth Century Society’s Spring lecture series (six in total) looks at the restoration and refurbishment of key C20 buildings in Britain and the US. Buildings covered: BBC Broadcasting House in London (G Val Meyer 1930-32, MacCormac Jamieson Prichard 2000-09). Speaker: Mark Hines (Mark Hines Architects), was the project architect and is the author of The Story of Broadcasting House: Home of the BBC. 5 February 2009. Crown Hall, Chicago (Mies van der Rohe 1952), the Art and Architecture Building, Yale University, New Haven (Paul Rudolf 1961-63) and the former Wills head office in Bristol (SOM with YRM 1970-75). Speaker: Patrick Bellew (Atelier 10 Engineers), 12 February 2009. Center for British Art, Yale University, New Haven (Louis Kahn 1969-77). Speaker: Peter Inskip (Inskip and Jenkins Architects), 17 February 2009. Brunswick Centre London (Patrick Hodgkinson 1967-72; Levitt Bernstein with Patrick Hodgkinson 2006). Speaker: Stuart Tappin (Stand Consulting Engineers Ltd), 26 February 2009. De La Warr Pavilion, Bexhill-on-Sea (Mendelsohn and Chermayeff 1934-5, John McAslan and Partners 2000-05). Speaker: Mark Cannata (HOK Architects), 5 March 2009. Finsbury Health Centre London (Lubetkin & Tecton 1938, first phase of conservation work Avanti Architects 1995.). Speaker: John Allan of Avanti Architects, 12 March 2009.

Second site

An exhibition by four artists from Roma/Gypsy/Traveller communities. [From the press release]

Second Metatarsophalangeal joint Synovitis: Update

In podiatric clinics is very common to find inflamatory process in metatarsophalangeal joint capsule , plantar plate and collateral ligaments damage, but it is not clearly recognized. Many authors hipotetized with joint instability of multiple aetiology and his concomitant evolution in different stages with own joint disease. This pathology has more incidence in second metatarsophalangeal joint than third and others and it is a common etiology of metatarsal pain. Bad biomechanics alters forefoot function and can produce overload in capsular joint, decreasing mobility and getting worse the pathology.