Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics

Background: Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. Results: Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP), and multicopy suppression (MSP) profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms), membrane functions (e.g. signalling, transport and targeting), membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. Conclusions: Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and that when COS and Fluconazole are used in combination they act in a synergistic fashion. The gene targets of COS identified in this study indicate that COS’s mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens.

Headspace solid-phase microextraction combined with mass spectrometry as a powerful analytical tool for profiling the terpenoid metabolomic pattern of hop-essential oil derived from Saaz variety

Hop(HumuluslupulusL.,Cannabaceaefamily)isprizedforitsessentialoilcontents,usedin beer production and, more recently, in biological and pharmacological applications. In this work,a methodinvolvingheadspace solid-phase microextractionand gas chromatography– mass spectrometry was developed and optimized to establish the terpenoid (monoterpenes and sesquiterpenes) metabolomic pattern of hop-essential oil derived from Saaz variety as a mean to explore this matrix as a powerful biological source for newer, more selective, biodegradable and naturally produced antimicrobial and antioxidant compounds. Different parameters affecting terpenoid metabolites extraction by headspace solid-phase microextraction were considered and optimized: type of fiber coatings, extraction temperature, extraction time, ionic strength, and sample agitation. In the optimized method, analytes were extracted for 30 min at 40 C in the sample headspace with a 50/30 m divinylbenzene/carboxen/polydimethylsiloxane coating fiber. The methodology allowed the identification of a total of 27 terpenoid metabolites, representing 92.5% of the total Saaz hop-essential oil volatile terpenoid composition. The headspace composition was dominated by monoterpenes (56.1%, 13 compounds), sesquiterpenes (34.9%, 10), oxygenated monoterpenes (1.41%, 3), and hemiterpenes (0.04%, 1) some of which can probably contribute to the hop of Saaz variety aroma. Mass spectrometry analysis revealed that the main metabolites are the monoterpene -myrcene (53.0±1.1% of the total volatile fraction), and the cyclic sesquiterpenes, -humulene (16.6 ± 0.8%), and -caryophyllene (14.7 ± 0.4%), which together represent about 80% of the total volatile fraction from the hop-essential oil. Thesefindingssuggestthatthismatrixcanbeexploredasapowerfulbiosourceofterpenoid metabolites.

Homeodomain-only protein HOP is a novel modulator of late differentiation in keratinocytes

The homeodomain-only protein (HOP) contains an atypical homeodomain which is unable to bind to DNA due to mutations in residues important for DNA binding. Recently, HOP was reported to regulate proliferation/differentiation homeostasis in different cell types. In the present study, we performed transcriptional profiling of cultured primary human keratinocytes and noted a robust induction of HOP upon calcium-induced cell differentiation. Immunohistochemistry of human skin localized HOP to the granular layer in the epidermis. Overexpression of HOP using a lentiviral vector up-regulated FLG and LOR expression during keratinocyte differentiation. Conversely, decreasing HOP expression using small interfering RNA markedly reduced the calcium-induced expression of late markers of differentiation in vitro, with the most prominent effect on profilaggrin (FLG) mRNA. Moreover, mRNA levels of profilaggrin and loricrin were downregulated in the epidermis of HOP knockout mice. Analysis of skin disorders revealed altered HOP expression in lichen planus, psoriasis and squamous cell carcinoma (SCC). Our data indicate that HOP is a novel modulator of late terminal differentiation in keratinocytes.

Homozygous deletion mapping in myeloma samples identifies genes and an expression signature relevant to pathogenesis and outcome.

PURPOSE: Myeloma is a clonal malignancy of plasma cells. Poor-prognosis risk is currently identified by clinical and cytogenetic features. However, these indicators do not capture all prognostic information. Gene expression analysis can be used to identify poor-prognosis patients and this can be improved by combination with information about DNA-level changes. EXPERIMENTAL DESIGN: Using single nucleotide polymorphism-based gene mapping in combination with global gene expression analysis, we have identified homozygous deletions in genes and networks that are relevant to myeloma pathogenesis and outcome. RESULTS: We identified 170 genes with homozygous deletions and corresponding loss of expression. Deletion within the "cell death" network was overrepresented and cases with these deletions had impaired overall survival. From further analysis of these events, we have generated an expression-based signature associated with shorter survival in 258 patients and confirmed this signature in data from two independent groups totaling 800 patients. We defined a gene expression signature of 97 cell death genes that reflects prognosis and confirmed this in two independent data sets. CONCLUSIONS: We developed a simple 6-gene expression signature from the 97-gene signature that can be used to identify poor-prognosis myeloma in the clinical environment. This signature could form the basis of future trials aimed at improving the outcome of poor-prognosis myeloma.

Task profiling : A task-Based approach to measuring the integration of ICT in the classroom

The measurement of ICT (information and communication technology) integration is emerging as an area of research interest with such systems as Education Queensland including it in their recently released list of research priorities. Studies to trial differing integration measurement instruments have taken place within Australia in the last few years, particularly Western Australia (Trinidad, Clarkson, & Newhouse, 2004; Trinidad, Newhouse & Clarkson, 2005), Tasmania (Fitzallen 2005) and Queensland (Finger, Proctor, & Watson, 2005). This paper will add to these investigations by describing an alternate and original methodological approach which was trialled in a small-scale pilot study conducted jointly by Queensland Catholic Education Commission (QCEC) and the Centre of Learning Innovation, Queensland University of Technology (QUT) in late 2005. The methodology described is based on tasks which, through a process of profiling, can be seen to be artefacts which embody the internal and external factors enabling and constraining ICT integration.

Computer profiling for forensic purposes

Computer forensics is the process of gathering and analysing evidence from computer systems to aid in the investigation of a crime. Typically, such investigations are undertaken by human forensic examiners using purpose-built software to discover evidence from a computer disk. This process is a manual one, and the time it takes for a forensic examiner to conduct such an investigation is proportional to the storage capacity of the computer's disk drives. The heterogeneity and complexity of various data formats stored on modern computer systems compounds the problems posed by the sheer volume of data. The decision to undertake a computer forensic examination of a computer system is a decision to commit significant quantities of a human examiner's time. Where there is no prior knowledge of the information contained on a computer system, this commitment of time and energy occurs with little idea of the potential benefit to the investigation. The key contribution of this research is the design and development of an automated process to describe a computer system and its activity for the purposes of a computer forensic investigation. The term proposed for this process is computer profiling. A model of a computer system and its activity has been developed over the course of this research. Using this model a computer system, which is the subj ect of investigation, can be automatically described in terms useful to a forensic investigator. The computer profiling process IS resilient to attempts to disguise malicious computer activity. This resilience is achieved by detecting inconsistencies in the information used to infer the apparent activity of the computer. The practicality of the computer profiling process has been demonstrated by a proof-of concept software implementation. The model and the prototype implementation utilising the model were tested with data from real computer systems. The resilience of the process to attempts to disguise malicious activity has also been demonstrated with practical experiments conducted with the same prototype software implementation.

A model for computer profiling

This paper discusses the use of models in automatic computer forensic analysis, and proposes and elaborates on a novel model for use in computer profiling, the computer profiling object model. The computer profiling object model is an information model which models a computer as objects with various attributes and inter-relationships. These together provide the information necessary for a human investigator or an automated reasoning engine to make judgements as to the probable usage and evidentiary value of a computer system. The computer profiling object model can be implemented so as to support automated analysis to provide an investigator with the information needed to decide whether manual analysis is required.

Devising a scenographic approach in Jonzi D's Hip Hop theatre

Jonzi D, one of the leading Hip Hop voices in the UK, creates contemporary theatrical works that merge dance, street art, original scored music and contemporary rap poetry, to create theatrical events that expand a thriving sense of a Hip Hop nation with citizens in the UK, throughout southern Africa and the rest of the world. In recent years Hip Hop has evolved as a performance genre in and of itself that not only borrows from other forms but vitally now contributes back to the body of contemporary practice in the performing arts. As part of this work Jonzi’s company Jonzi D Productions is committed to creating and touring original Hip Hop theatre that promotes the continuing development and awareness of a nation with its own language, culture and currency that exists without borders. Through the deployment of a universal voice from the local streets of Johannesburg and the East End of London, Jonzi D creates a form of highly energized performance that elevates Hip Hop as great democratiser between the highly developed global and under resourced local in the world. It is the staging of this democratised and technologised future (and present), that poses the greatest challenge for the scenographer working with Jonzi and his company, and the associated deprogramming and translation of the artists particular filmic vision to the stage, that this discussion will explore. This paper interrogates not only how a scenographic strategy can support the existence of this work but also how the scenographer as outsider can enter and influence this nation.

Dealing with temporal inconsistency in automated computer forensic profiling

Computer profiling is the automated forensic examination of a computer system in order to provide a human investigator with a characterisation of the activities that have taken place on that system. As part of this process, the logical components of the computer system – components such as users, files and applications - are enumerated and the relationships between them discovered and reported. This information is enriched with traces of historical activity drawn from system logs and from evidence of events found in the computer file system. A potential problem with the use of such information is that some of it may be inconsistent and contradictory thus compromising its value. This work examines the impact of temporal inconsistency in such information and discusses two types of temporal inconsistency that may arise – inconsistency arising out of the normal errant behaviour of a computer system, and inconsistency arising out of deliberate tampering by a suspect – and techniques for dealing with inconsistencies of the latter kind. We examine the impact of deliberate tampering through experiments conducted with prototype computer profiling software. Based on the results of these experiments, we discuss techniques which can be employed in computer profiling to deal with such temporal inconsistencies.