Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Notch and NOXA-related pathways in melanoma cells

Notch receptor-mediated intracellular events represent an ancient cell signaling system, and alterations in Notch expression are associated with various malignancies in which Notch may function as an oncogene or less commonly as a tumor suppressor. Notch signaling regulates cell fate decisions in the epidermis, including influencing stem cell dynamics and growth/differentiation control of cells in skin. Because of increasing evidence that the Notch signaling network is deregulated in human malignancies, Notch receptors have become attractive targets for selective killing of malignant cells. Compared with proliferating normal human melanocytes, melanoma cell lines are characterized by markedly enhanced levels of activated Notch-1 receptor. By using a small molecule gamma-secretase inhibitor (GSI) consisting of a tripeptide aldehyde, N-benzyloxycarbonyl-Leu-Leu-Nle-CHO, which can block processing and activation of all four different Notch receptors, we identified a specific apoptotic vulnerability in melanoma cells. GSI triggers apoptosis in melanoma cells, but only G2/M growth arrest in melanocytes without subsequent cell death. Moreover, GSI treatment induced a pro-apoptotic BH3-only protein, NOXA, in melanoma cells but not in normal melanocytes. The use of GSI to induce NOXA induction overcomes the apoptotic resistance of melanoma cells, which commonly express numerous cell survival proteins such as Mcl-1, Bcl-2, and survivin. Taken together, these results highlight the concept of synthetic lethality in which exposure to GSI, in combination with melanoma cells overexpressing activated Notch receptors, has lethal consequences, producing selective killing of melanoma cells, while sparing normal melanocytes. By identifying signaling pathways that contribute to the transformation of melanoma cells (e.g. Notch signaling), and anti-cancer agents that achieve tumor selectivity (e.g., GSI-induced NOXA), this experimental approach provides a useful framework for future therapeutic strategies in cutaneous oncology.

The Global Youth Media Council : young people speaking and learning about media reform

The 5th World Summit on Media for Children and Youth held in Karlstad, Sweden in June 2010 provided a unique media literacy experience for approximately thirty young people from diverse backgrounds through participation in the Global Youth Media Council. This article focuses on the Summit’s aim to give young people a ‘voice’ through intercultural dialogue about media reform. The accounts of four young Australians are discussed in order to consider how successful the Summit was in achieving this goal. The article concludes by making recommendations for future international media literacy conferences involving young people. It also advocates for the expansion of the Global Youth Media Council concept as a grass roots movement to involve more young people in discussions about media reform.

Conceptualising climate change in rural Australia : community perceptions, attitudes and (in) actions

Public engagement and support is essential for ensuring adaptation to climate change. The first step in achieving engagement is documenting how the general public currently perceive and understand climate change issues, specifically the importance they place on this global problem and identifying any unique challenges for individual communities. For rural communities, which rely heavily on local agriculture industries, climate change brings both potential impacts and opportunities. Yet, to date, our knowledge about how rural residents conceptualise climate change is limited. Thus, this research explores how the broader rural community – not only farmers – conceptualise climate change and responsive activities, focussing on documenting the understandings and risk perceptions of local residents from two small Australian rural communities. Twenty-three semi-structured interviews were conducted in communities in the Eden/Gippsland region on the border of New South Wales and Victoria, and the North-East of Tasmania. There are conflicting views on how climate change is conceptualised, the degree of concern and need for action, the role of local industry, who will 'win' and 'lose', and the willingness of rural communities to adapt. In particular, residents who believed in anthropogenic or human-induced factors described the changing climate as evidence of 'climate change', whereas those who were more sceptical termed it 'weather variability', suggesting that there is a divide in rural Australia that, unless urgently addressed, will hinder local and national policy responses to this global issue. Engaging these communities in the 21st century climate change debate will require a significant change in terminology and communication strategies.

Three theories and a process: engaging community

This study examines a dialogue process managers can use to explore community attitudes. The objectives of the research are to develop a dialogue process that engages community audiences on climate mitigation strategies. Secondly, to understand participants perspectives and potential reactions in particular to underground storage of CO2 and determine the strategies that most effectively engage people in dialogue to enable the climate change debate to move forward. Finally, to develop a dialogue process that can be used by managers on other politically sensitive topics. Knowledge of the dynamics of psychosocial relationships and communication between stakeholders contributed to increased understanding of the issues. The key findings of this study indicate that the public can be engaged in dialogue on the issue of CO2 capture and storage and low emission technologies without engendering adverse reactions. The dialogue process is critical to participant’s engagement and led to behaviour change in energy use.

The mobile phone : the new communication drum of Papua New Guinea

This thesis examines the role of mobile telephony in rural communities in Papua New Guinea (PNG). It is a threshold study which reports on research conducted in the earliest stages of mobile phone adoption in these areas. It explores the ways in which this new technology changes people’s lives, social structures and relationships. The research focuses on non-urban communities, which previously had little or no access to modern communication technologies, but which are in some cases still using traditional forms of communication such as drums. It has found that the introduction of mobile telecommunications has generally been viewed positively, although several negative concerns have been strongly felt. Specific benefits related to enhanced communication with relatives and friends living away from home villages, and use of the technology in time-critical emergencies or crises. Difficulties have arisen with respect to the cost of owning and operating a handset, as well as financial and logistical challenges when recharging handset batteries, particularly in areas with no mains electricity supply. Perceived damaging effects of mobile phone access related to sex, crime and pornography. The changes taking place are described through a social lens, by foregrounding the perceptions of villagers. The perspectives of key informants, such as telecommunication company managers, are also discussed. Employing the technique of triangulation (using different methods and sources) has helped to validate the findings of the research project. The sources constantly overlap and agree on the main themes, such as those outlined above. PNG is a developing country which performs poorly on a wide range of development indicators. A large majority of the people live outside of the major towns and cities. It is therefore worthwhile investigating the introduction of mobile phone technology in rural areas. These areas often have poor access to services, including transport, health, education and banking. Until 2007, communities in such regions fell outside of mobile phone coverage areas. In the case of all ten villages discussed in this thesis, there has never been any landline telephone infrastructure available. Therefore, this research on mobile phones is in effect documenting the first ever access to any kind of phone in these communities. This research makes a unique contribution to knowledge about the role of communication in PNG, and has implications for policy, practice and theory. In the policy arena, the thesis aids understanding of the impact which communication sector competition and regulation can have on rural and relatively isolated communities. There are three practical problems which have emerged from the research: cost, battery recharging difficulties and breakage are all major obstacles to uptake and use of mobile telephony in rural communities. Efforts to reduce usage costs, enable easier recharging, and design more robust handsets would allow for increased utilisation of mobile phones for a range of purposes. With respect to the realm of theory, this research sits amongst the most recent scholarship in the mobile phone field, located within the broader communication theory area. It recommends cautionary reading of any literature which suggests that mobile phones will reduce poverty and increase incomes in poor, rural communities in developing countries. Nonetheless, the present research adds weight to mobile phone studies which suggest that the primary advantages of mobile phones in such settings are for the satisfactions of communication of itself, and for social interaction among loved ones.

Urban food futures : ICTs and opportunities

Food is a vital foundation of all human life. It is essential to a myriad of political, socio-cultural, economic and environmental practices throughout history. However, those practices of food production, consumption, and distribution have the potential to now go through immensely transformative shifts as network technologies become increasingly embedded in every domain of contemporary life. Information and communication technologies (ICTs) are one of the key foundations of global functionality and sustenance today and undoubtedly will continue to present new challenges and opportunities for the future. As such, this Symposium will bring together leading scholars across disciplines to address challenges and opportunities at the intersection of food and ICTs in everyday urban environment. In particular, the discussion will revolve around the question: What are the key roles that network technologies play in re-shaping the food systems at micro- to macroscopic level? The symposium will contribute a unique perspective on urban food futures through the lens of network society paradigm where ICTs enable innovations in production, organisation, and communication within society. Some of the topics addressed will include encouraging transparency in food commodity chains; value of cultural understanding and communication in global food sustainability; and technologies to social inclusion; all of which evoke and examine the question surrounding networked individuals as changes catalysts for urban food futures. The event will provide an avenue for new discussions and speculations on key issues surrounding urban food futures in the network era, with a particular focus on bottom-up micro actions that challenge the existing food systems towards a broader sociocultural, political, technological, and environmental transformations. One central area of concern is that current systems of food production, distribution, and consumption do not ensure food security for the future, but rather seriously threaten it. With the recent unprecedented scale of urban growth and rise of middle-class, the problem continues to intensify. This situation requires extensive distribution networks to feed urban residents, and therefore poses significant infrastructural challenges to both the public and private sectors. The symposium will also address the transferability of citizen empowerment that network technologies enable as demonstrated in various significant global political transformations from the bottom-up, such as the recent Egyptian Youth Revolution. Another key theme of the discussion will be the role of ICTs (and the practices that they mediate) in fostering transparency in commodity chains. The symposium will ask what differences these technologies can make on the practices of food consumption and production. After discussions, we will initiate an international network of food-thinkers and actors that will function as a platform for knowledge sharing and collaborations. The participants will be invited to engage in planning for the on-going future development of the network.

Looking through the corridor : Malaysia and the MSC

As part of a development plan-in-progress spanning a total of 25 years(1996 to 2020), Malaysia’s Multimedia Super Corridor (MSC) provides a unique opportunity to witness a brief and microcosmic unfolding of the reciprocally formative process between society and technology that Lewis Mumford lays out in exhaustive detail in Technics and Civilization (Mumford, 1963). The interlocking of national imagining, destiny and progress with a specific group of technologies, information and communication technologies(ICT) is, in itself, worthy of interest. However, what renders the MSC doubly remarkable is its introduction in Malaysia, one of the most well established of contemporary ethnocracies. This chapter reads the development and implementation of the MSC as the text through which the association between nation and ethnicity is examined. Broadly speaking I argue here that the MSC inflects the imagining(s) of Malaysia at two levels. At the first level where the MSC is understood to be the insertion of a new policy into Malaysia’s pre existent ethnocratic climate, I contend the MSC inflects the nation through its incongruence with prevalent conditions. At the second level, where the MSC is viewed through the position of its Chinese populace, I suggest that the MSC inflects Malaysia (perhaps to a lesser degree) through the re-emphasis it lends to issues of transnationalism and belonging for the Malaysian Chinese.

Cultural chaos : Journalism, News and Power in a Globalised World

With examples drawn from media coverage of the War on Terror, the 2003 invasion of Iraq, Hurricane Katrina and the London underground bombings, Cultural Chaos explores the changing relationship between journalism and power in an increasingly globalised news culture. In this new text, Brian McNair examines the processes of cultural, geographic and political dissolution in the post-Cold War era and the rapid evolution of information and communication technologies. He investigates the impact of these trends on domestic and international journalism and on political processes in democratic and authoritarian societies across the world. Written in a lively and accessible style, Cultural Chaos provides students with an overview of the evolution of the sociology of journalism, a critical review of current thinking within media studies and an argument for a revision and renewal of the paradigms that have dominated the field since the early twentieth century. Separate chapters are devoted to new developments such as the rise of the blogosphere and satellite television news and their impact on journalism more generally. Cultural Chaos will be essential reading for all those interested in the emerging globalised news culture of the twenty-first century.

Using cost-effective multimedia to create engaging learning experiences in law and other disciplines

This is the final report of an Australian Learning and Teaching Council Teaching Fellowship which addressed the needs of two separate groups of learners: (1) final year law students studying ethics and (2) law academics and other interested educators in higher education wishing to use information and communication technologies (ICT) to create engaging learning environments for their students but lacking the capacity to do so. The Fellowship resulted in final year law students being infused with an improved appreciation of ethical practice than they receive from traditional lecture/tutorial means by the development of an integrated program of blended learning including an online program entitled "Entry into Valhalla". This "ethics capstone‟ utilises multimedia produced using cost effective resources (including the "Second Life" virtual environment) to create engaging, contextualised learning experiences. The Fellowship also constructed the knowledge of producing cost-effective multimedia projects in other law academics and other educators in higher education by staff development activities comprising workshops, conference presentations and an interactive website using the "Entry into Valhalla" program as a case study exemplar.

On IT governance structures and their effectiveness in collaborative organizational structures

Organizations today engage in various forms of alliances to manage their existing business processes or to diversify into new processes to sustain their competitive positions. Many of today’s alliances use the IT resources as their backbone. The results of these alliances are collaborative organizational structures with little or no ownership stakes between the parties. The emergence of Web 2.0 tools is having a profound effect on the nature and form of these alliance structures. These alliances heavily depend on and make radical use of the IT resources in a collaborative environment. This situation requires a deeper understanding of the governance of these IT resources to ensure the sustainability of the collaborative organizational structures. This study first suggests the types of IT governance structures required for collaborative organizational structures. Semi-structured interviews with senior executives who operate in such alliances reveal that co-created IT governance structures are necessary. Such structures include co-created IT-steering committees, co-created operational committees, and inter-organizational performance management and communication systems. The findings paved the way for the development of a model for understanding approaches to governing IT and evaluating the effectiveness for such governance mechanisms in today’s IT dependent alliances. This study presents a sustainable IT-related capabilities approach to assessing the effectiveness of suggested IT governance structures for collaborative alliances. The findings indicate a favourable association between organizations IT governance efforts and their ability to sustain their capabilities to leverage their IT resources. These IT-related capabilities also relate to measures business value at the process and firm level. This makes it possible to infer that collaborative organizations’ IT governance efforts contribute to business value.

Towards human and social innovation: not wanting to know in order to create

The formation of a venture relies, in part, upon the participants reaching a shared understanding of purpose and process. Yet in circumstances of great complexity and uncertainty how can such a shared understanding be created? If the response to complexity and uncertainty is to seek simplicity in order to find commonality then what is lost and what is at risk? Can shared understandings of purpose and process be arrived at by embracing complexity and uncertainty and if so how? These questions led us to explore the process of dialogue and communication of a team in its formative stages. Our interests were not centred upon the behavioural characteristics of the individuals in the 'forming' stage of group dynamics but rather the process of cognitive and linguistic turns, the wax and wan of ideas and, the formation of shared meaning. This process of cognitive and linguistic turns was focused thematically on the areas of foresight, innovation, entrepreneurship, and public policy. This cross disciplinary exploration sought to explore potential synergies between these domains, in particular in developing a conceptual basis for long term thinking that can inform wiser public policy.

Professional capabilities for twenty-first century creative careers : lessons from outstandingly successful Australian artists and designers

Artists and designers are positioned at the centre of the 21st century creative economy. In order to recognise and make the most of the opportunities afforded by this new era, artists and designers still require the creativity, disciplinary depth of knowledge, and technical skills traditionally possessed by professionals in these fields – skills which are a core strength of higher and further art and design education. However, they may also require a range of other, ‘21st century’ creative capabilities which are harder to define, teach for and assess, and are not the focus of traditional art and design pedagogies. This article draws upon the findings of nine in-depth interviews with award-winning Australian artists and designers about their careers and working practices, along with recent international research about the characteristics of the 21st century creative career, in order to highlight the importance of certain professional capabilities for art and design. It discusses the implications of these findings for art and design educators in universities, and curricular and pedagogic considerations associated with embedding these capabilities into undergraduate courses.