Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E-coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms. (c) 2005 Elsevier Ltd. All rights reserved.

The cyclotides and related macrocyclic peptides as scaffolds in drug design

The applicability of linear peptides as drugs is potentially limited by their susceptibility to proteolytic cleavage and poor bioavailability. Cyclotides are macrocyclic cystine-knotted mini-proteins that have a broad range of bioactivities and are exceptionally stable, being resistant to chemical, thermal and enzymatic degradation. The general limitations of peptides as drugs can potentially be overcome by using the cyclotide framework as a scaffold onto which new activities may be engineered. The potential use of cyclotides and related peptide scaffolds for drug design is evaluated herein, with reference to increasing knowledge of the structures and sequence diversity of natural cyclotides and the emergence of new approaches in protein engineering.

Balancing curriculum processes and content in a project centred curriculum - In pursuit of graduate attributes

Chemical engineering education is challenged around the world by demands and rapid changes encompassing a wide range of technical and social drivers. Graduates must be prepared for practice in increasingly diverse workplace environments in which generic or transferable attributes such as communication and teamwork together with technical excellence are mandated by prospective employers and society at large. If academe is to successfully deliver on these graduate attributes, effective curriculum design needs to include appropriate educational processes as well as course content. Conventional teacher centred approaches, stand-alone courses and retro-fitted remedial modules have not delivered the desired outcomes. Development of the broader spectrum of attributes is more likely when students are engaged with realistic and relevant experiences that demand the integration and practice of these attributes in contexts that the students find meaningful. This paper describes and evaluates The University of Queensland's Project Centred Curriculum in Chemical Engineering (PCC), a programme-wide approach to meeting these requirements. PCC strategically integrates project-based learning with more traditional instruction. Data collected shows improved levels of student attainment of generic skills with institutional and nationally benchmarked indicators showing significant increases in student perceptions of teaching quality, and overall satisfaction with the undergraduate experience. Endorsements from Australian academic, professional and industry bodies also support the approach as more effectively aligning engineering education with professional practice requirements.

Proceedings of the 2004 Australian Software Engineering Conference

Established in 1986, ASWEC is the premier technical meeting for the Australian Software Engineering Community, and attracts a significant number of international participants. The conference is sponsored by both Engineers Australia and the Australian Computer Society. The major goal of the conference is to provide a forum for exchanging experience and new research results in software engineering. The technical program for ASWEC 2004 includes research papers from Australia and across the world. This year we received 79 submissions from 12 countries: 56 from Australia, 6 from New Zealand, 9 from Asia, 4 from Europe, and 4 from North America. All papers were fully refereed by three (two papers by only two) Program Committee members. We accepted 36 papers to be presented at the conference. We are grateful to all authors who contributed to ASWEC 2004. In addition to the technical papers, the conference program also includes two keynote speakers and one panel on Software Engineering accreditation. We are very pleased about being able to attract Philippe Kruchten, University of British Columbia, and Ian Hayes, The University of Queensland, as the keynote speakers for this conference.

Proceedings of the 2005 Australian Software Engineering Conference

Established in 1986, ASWEC is the premier technical meeting for the Australian software engineering community, and attracts a significant number of international participants. The major goal of the conference is to provide a forum for exchanging experience and new research results in software engineering. To increase the industry participation at ASWEC, we organized two separate paper tracks, which we have called Research Papers and Industry Experience Reports. These paper tracks had separate deadlines, separate program committees, separate review procedures, and separate proceedings. The Research Papers appear in these proceedings and the Industry Experience Reports will appear on a CD-Rom that will be distributed at the conference. The Research Papers track for ASWEC 2005 includes submissions from Australia and across the world. This year we received 79 submissions from 13 countries: 48 from Australia, 7 from New Zealand, 11 from Asia, 9 from Europe, and 2 each from North and South America. All papers were fully refereed by three Program Committee members. We accepted 34 papers to be presented at the conference. We are grateful to all authors who contributed to ASWEC.