Drosophila 3′ UTRs are more complex than protein-coding sequences

The 3′ UTRs of eukaryotic genes participate in a variety of post-transcriptional (and some transcriptional) regulatory interactions. Some of these interactions are well characterised, but an undetermined number remain to be discovered. While some regulatory sequences in 3′ UTRs may be conserved over long evolutionary time scales, others may have only ephemeral functional significance as regulatory profiles respond to changing selective pressures. Here we propose a sensitive segmentation methodology for investigating patterns of composition and conservation in 3′ UTRs based on comparison of closely related species. We describe encodings of pairwise and three-way alignments integrating information about conservation, GC content and transition/transversion ratios and apply the method to three closely related Drosophila species: D. melanogaster, D. simulans and D. yakuba. Incorporating multiple data types greatly increased the number of segment classes identified compared to similar methods based on conservation or GC content alone. We propose that the number of segments and number of types of segment identified by the method can be used as proxies for functional complexity. Our main finding is that the number of segments and segment classes identified in 3′ UTRs is greater than in the same length of protein-coding sequence, suggesting greater functional complexity in 3′ UTRs. There is thus a need for sustained and extensive efforts by bioinformaticians to delineate functional elements in this important genomic fraction. C code, data and results are available upon request.

Cutting the Gordian knot of futility : a case for law reform on unilateral withholding and withdrawal of potentially life-sustaining treatment

In this paper, we propose law reform with respect to the unilateral withholding or withdrawal of potentially life-sustaining treatment in Australia and New Zealand. That is, where a doctor withholds or withdraws potentially life-sustaining treatment without consent from a patient or a patient’s substitute decision-maker (where the patient lacks capacity), or authorisation from a court or tribunal, or by operation of a statute or justifiable government or institutional policy. Our proposal is grounded in the core values that do (or should) underpin a regulatory framework on an issue such as this; these values are drawn from existing commitments made by Australia and New Zealand through legislation, the common law, and conventions and treaties. It is also grounded in a critical review of the law on unilateral withholding and withdrawal as well as the legal context within which this issue sits in Australasia. We argue that the current law is inconsistent with the core values and develop a proposal for a legal response to this issue that more closely aligns with the core values it is supposed to serve.

Offspring of mothers fed a high fat diet display hepatic cell cycle inhibition and associated changes in gene expression and DNA methylation

The association between an adverse early life environment and increased susceptibility to later-life metabolic disorders such as obesity, type 2 diabetes and cardiovascular disease is described by the developmental origins of health and disease hypothesis. Employing a rat model of maternal high fat (MHF) nutrition, we recently reported that offspring born to MHF mothers are small at birth and develop a postnatal phenotype that closely resembles that of the human metabolic syndrome. Livers of offspring born to MHF mothers also display a fatty phenotype reflecting hepatic steatosis and characteristics of non-alcoholic fatty liver disease. In the present study we hypothesised that a MHF diet leads to altered regulation of liver development in offspring; a derangement that may be detectable during early postnatal life. Livers were collected at postnatal days 2 (P2) and 27 (P27) from male offspring of control and MHF mothers (n = 8 per group). Cell cycle dynamics, measured by flow cytometry, revealed significant G0/G1 arrest in the livers of P2 offspring born to MHF mothers, associated with an increased expression of the hepatic cell cycle inhibitor Cdkn1a. In P2 livers, Cdkn1a was hypomethylated at specific CpG dinucleotides and first exon in offspring of MHF mothers and was shown to correlate with a demonstrable increase in mRNA expression levels. These modifications at P2 preceded observable reductions in liver weight and liver:brain weight ratio at P27, but there were no persistent changes in cell cycle dynamics or DNA methylation in MHF offspring at this time. Since Cdkn1a up-regulation has been associated with hepatocyte growth in pathologic states, our data may be suggestive of early hepatic dysfunction in neonates born to high fat fed mothers. It is likely that these offspring are predisposed to long-term hepatic dysfunction.

Identification of optimal epitopes for Plasmodium falciparum rapid diagnostic tests that target histidine-rich proteins 2 and 3

Rapid diagnostic tests (RDTs) represent important tools to diagnose malaria infection. To improve understanding of the variable performance of RDTs that detect the major target in Plasmodium falciparum, namely, histidine-rich protein 2 (HRP2), and to inform the design of better tests, we undertook detailed mapping of the epitopes recognized by eight HRP-specific monoclonal antibodies (MAbs). To investigate the geographic skewing of this polymorphic protein, we analyzed the distribution of these epitopes in parasites from geographically diverse areas. To identify an ideal amino acid motif for a MAb to target in HRP2 and in the related protein HRP3, we used a purpose-designed script to perform bioinformatic analysis of 448 distinct gene sequences from pfhrp2 and from 99 sequences from the closely related gene pfhrp3. The frequency and distribution of these motifs were also compared to the MAb epitopes. Heat stability testing of MAbs immobilized on nitrocellulose membranes was also performed. Results of these experiments enabled the identification of MAbs with the most desirable characteristics for inclusion in RDTs, including copy number and coverage of target epitopes, geographic skewing, heat stability, and match with the most abundant amino acid motifs identified. This study therefore informs the selection of MAbs to include in malaria RDTs as well as in the generation of improved MAbs that should improve the performance of HRP-detecting malaria RDTs.

Blood transfer devices for malaria rapid diagnostic tests : evaluation of accuracy, safety and ease of use

Background: Malaria rapid diagnostic tests (RDTs) are increasingly used by remote health personnel with minimal training in laboratory techniques. RDTs must, therefore, be as simple, safe and reliable as possible. Transfer of blood from the patient to the RDT is critical to safety and accuracy, and poses a significant challenge to many users. Blood transfer devices were evaluated for accuracy and precision of volume transferred, safety and ease of use, to identify the most appropriate devices for use with RDTs in routine clinical care. Methods: Five devices, a loop, straw-pipette, calibrated pipette, glass capillary tube, and a new inverted cup device, were evaluated in Nigeria, the Philippines and Uganda. The 227 participating health workers used each device to transfer blood from a simulated finger-prick site to filter paper. For each transfer, the number of attempts required to collect and deposit blood and any spilling of blood during transfer were recorded. Perceptions of ease of use and safety of each device were recorded for each participant. Blood volume transferred was calculated from the area of blood spots deposited on filter paper. Results: The overall mean volumes transferred by devices differed significantly from the target volume of 5 microliters (p < 0.001). The inverted cup (4.6 microliters) most closely approximated the target volume. The glass capillary was excluded from volume analysis as the estimation method used is not compatible with this device. The calibrated pipette accounted for the largest proportion of blood exposures (23/225, 10%); exposures ranged from 2% to 6% for the other four devices. The inverted cup was considered easiest to use in blood collection (206/ 226, 91%); the straw-pipette and calibrated pipette were rated lowest (143/225 [64%] and 135/225 [60%] respectively). Overall, the inverted cup was the most preferred device (72%, 163/227), followed by the loop (61%, 138/227). Conclusions: The performance of blood transfer devices varied in this evaluation of accuracy, blood safety, ease of use, and user preference. The inverted cup design achieved the highest overall performance, while the loop also performed well. These findings have relevance for any point-of-care diagnostics that require blood sampling.

High mobility diketopyrrolopyrrole (DPP)-based organic semiconductor materials for organic thin film transistors and photovoltaics

In recent years, the electron-accepting diketopyrrolopyrrole (DPP) moiety has been receiving considerable attention for constructing donor-acceptor (D-A) type organic semiconductors for a variety of applications, particularly for organic thin film transistors (OTFTs) and organic photovoltaics (OPVs). Through association of the DPP unit with appropriate electron donating building blocks, the resulting D-A molecules interact strongly in the solid state through intermolecular D-A and π-π interactions, leading to highly ordered structures at the molecular and microscopic levels. The closely packed molecules and crystalline domains are beneficial for intermolecular and interdomain (or intergranular) charge transport. Furthermore, the energy levels can be readily adjusted, affording p-type, n-type, or ambipolar organic semiconductors with highly efficient charge transport properties in OTFTs. In the past few years, a number of DPP-based small molecular and polymeric semiconductors have been reported to show mobility close to or greater than 1 cm2 V -1 s-1. DPP-based polymer semiconductors have achieved record high mobility values for p-type (hole mobility: 10.5 cm2 V-1 s-1), n-type (electron mobility: 3 cm2 V-1 s-1), and ambipolar (hole/electron mobilities: 1.18/1.86 cm2 V-1 s-1) OTFTs among the known polymer semiconductors. Many DPP-based organic semiconductors have favourable energy levels and band gaps along with high hole mobility, which enable them as promising donor materials for OPVs. Power conversion efficiencies (PCE) of up to 6.05% were achieved for OPVs using DPP-based polymers, demonstrating their potential usefulness for the organic solar cell technology. This article provides an overview of the recent exciting progress made in DPP-containing polymers and small molecules that have shown high charge carrier mobility, around 0.1 cm2 V-1 s-1 or greater. It focuses on the structural design, optoelectronic properties, molecular organization, morphology, as well as performances in OTFTs and OPVs of these high mobility DPP-based materials.

Aboriginal and Torres Strait Islander university students conceptions of formal learning and experiences of informal learning

This paper describes an investigation of conceptions of learning held by 22 Aboriginal and Torres Strait Islander students from three universities in Queensland, Australia. Other areas investigated were students' experiences of informal learning, their reasons for studying and the strategies they used to learn. Research into conceptions of learning is gaining impetus and current beliefs include the premise that approaches to learning adopted by university students, and hence learning outcomes, are closely related to their conceptions of learning. There is substantial research focused on Aboriginal learning styles in early childhood and primary school which indicates that Aboriginal children prefer to learn in a practical way as well as through observation and imitation and trial and error. Very little research has focused specifically on Aboriginal university students' conceptions of learning. Results of this study found that these students view and approach formal university learning in much the same way as other university students and most hold quantitative conceptions of learning. The most interesting result was the difference between students' conceptions of formal learning and their experiences of informal learning. Many students' experiences of informal learning were grounded in practical activities or exhibited a cultural focus, however, most formal learning is not dependent upon practical or cultural knowledge. It is proposed that formal learning for Indigenous students recognise and include an Indigenous perspective such as integrating, where appropriate, practical strategies for learning. We also suggest that Indigenous students be helped to develop conceptions that will enable them to learn formal, theoretical material successfully.

Learning in and out of university : Aboriginal and Torres Strait Islander students’ conceptions and strategies used to learn

Research suggests that students’ approaches to learning and learning outcomes are closely related to their conceptions of learning. This paper describes a phenomenographically inspired investigation into conceptions of formal learning held by 22 Aboriginal and Torres Strait Islander students from three Australian universities in Queensland; experiences of informal learning, reasons for studying and strategies used to learn were also investigated. The attrition rate for these students in tertiary education is higher than that of any other group of students. It was hoped that information gained may delineate factors that contribute to high attrition rates and therefore inform courses of action that may lead to improved teaching and learning practices for these students. Additionally, success in tertiary education for Aboriginal and Torres Strait Islander students may increase their involvement in mainstream society. Results showed that they view and approach university learning in much the same way as other university students. It was also apparent that, generally, the strategies these students used did not match the conceptions of learning they held. An interesting result was the difference between the conceptions of formal learning and explanations of informal learning

Learning in formal and informal contexts : conceptions and strategies of Aboriginal and Torres Strait Islander university students

Research suggests that students' approaches to learning and hence learning outcomes are closely related to their conceptions of learning. This paper describes an investigation into conceptions of formal learning held by 22 Aboriginal and Torres Strait Islander students from three Australian universities in Queensland; categories of informal learning, reasons for studying and strategies used to learn were also investigated. The attrition rate for these students in tertiary education is higher than that of any other group of students. The main aim of this study was to determine their conceptions of learning in order to provide information that might facilitate instruction more suited to their needs in order to address the high attrition rate. Results showed that these students view and approach university learning in much the same way as other university students. It was also apparent that, for the most part, the strategies these students used did not match the conceptions of learning they held. An interesting result was the difference between the conceptions of formal learning and perceptions of informal learning.

Best of breed IT strategy: an alternative to enterprise resource planning systems

Abstract - Enterprise Resource Planning (ERP) software has become the dominant strategic platform for supporting enterprise-wide business processes. However, single vendor ERP software systems have been criticised for not meeting specific organisation and industry requirements. An alternative approach ‘Best of Breed (BoB)’, integrates components of software from multiple standard package vendors, and in some cases custom components. The objective is to develop enterprise systems that are more closely aligned with the requirements of an organisation. Although this approach may not be common at present it is likely to grow in importance due to business needs and technology advances such as the componentisation of ERP software. A case study analysis of a BoB implementation at a global entertainment's company is used as a platform for the discussion of the issues associated with this strategy and a comparison is made with the single vendor ERP alternative. The analysis centres on the complexity of implementation, the differences in the levels of functionality and business fit and the maintenance requirements.

ERP and best of breed : a comparative analysis

Enterprise Resource Planning (ERP) software is the dominant strategic platform for supporting enterprise-wide business processes. However, it has been criticised for being inflexible and not meeting specific organisation and industry requirements. An alternative, Best of Breed (BoB), integrates components of standard package and/or custom software. The objective is to develop enterprise systems that are more closely aligned with the business processes of an organisation. A case study of a BoB implementation facilitates a comparative analysis of the issues associated with this strategy and the single vendor ERP alternative. The paper illustrates the differences in complexity of implementation, levels of functionality, business process alignment potential and associated maintenance.

‘It's all scientific to me’ : focus group insights into why young people do not apply safe-sex knowledge

Despite rising levels of safe-sex knowledge in Australia, sexually transmitted infection notifications continue to increase. A culture-centred approach suggests it is useful in attempting to reach a target population first to understand their perspective on the issues. Twenty focus groups were conducted with 89 young people between the ages of 14 and 16 years. Key findings suggest that scientific information does not articulate closely with everyday practice, that young people get the message that sex is bad and they should not be preparing for it and that it is not appropriate to talk about sex. Understanding how young people think about these issues is particularly important because the focus groups also found that young people disengage from sources of information that do not match their own experiences.

Straminipilan protists : a study of their taxonomic position, morphology and abiotic stress-mediated gene expression

Thraustochytrids have become of considerable industrial and scientific interest in the past decade due to their health benefits. They have been proven to be the principle source in marine and estuarine fish diets with high percentage of long chain (LC) or polyunsaturated fatty acids (PUFA). Therefore, the oil extracted from fish for human document.forms[0].elements[13].select();consumption is rich in PUFA with high omega-3 fatty acid content. Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) of all of the omega-3 fatty acids, are considered beneficial essential oils for humans with a wide range of health benefits. These include brain and neural development in infants, general wellbeing of adults and drug delivery through precursor molecules. They have become one of the most extensively studied organisms for industrial oil preparations as PUFA extraction from fish becomes less profitable. Many forms of these Thraustochytrid oils are being trialled for human consumption all over the world. In Australia, there has been little research performed on these organisms in the past ten years. A few Australian studies have been conducted in the form of comparative studies related to PUFA production within the related genera, but not focussed on their identification or cellular and genomic characterisation. Therefore, the main aim of this study was to investigate the morphological and genetic characteristics of Australian Thraustochytrids in order to aid in their identification and characterisation, as well as to better understand the effect of environmental conditions in the regulation of PUFA production. It was also noted that there was a knowledge gap in the preservation and total genomic DNA extraction of these organisms for the purposes of scientific research. The cryopreservation of these organisms for studies around the world follows existing generic methods. However, it is well understood that many of these generic methods attract not only high costs for chemicals, but also uses considerable storage space and other resources, all of which can be improved with new or modified approaches. In this context, a simple and inexpensive bead preservation method is described, without compromising the storage shelf life. We also describe, for the first time, the effects of culture age on the successful cryopreservation of Thraustochytrids. It was evident in the literature that DNA and RNA extractions for molecular and genetic studies of Thraustochytrids follow the classical phenol-chloroform extraction methods. It was also observed that modern protocols failed to avoid the use of phenol-chloroform rather than improving preparation and cell disruption. In order to provide a high quantity and quality DNA extraction, a modified protocol has been introduced that employs the use of modern commercial extraction kits and standard laboratory equipment. Thraustochytrids have been shown to be highly conserved in their 18S rDNA gene sequences, which is used as the current standard for identification. It was demonstrated that the 18S rDNA gene sequence limits the recognition of closely related genera or within the genera from each member. Therefore, it was proposed that another profile, such as a randomly amplified polymorphic DNA (RAPD) based profiling system, be tested for use in the characterisation of Thraustochytrids. The RAPD profiles were shown to provide a unique DNA fingerprint for each isolate and small variations in their genome were able to be detected. This method involved the use of a minimum number of standard arbitrary primers and with an increase in the number of different primers used, a very high discrimination between organisms could be achieved. However, the method was not suitable for taxonomic purposes because the results did not correlate with other taxonomic features such as morphology. Another knowledge gap was found with respect to Australian Thraustochytrid growth characteristics, in that these had not been recorded and published. In order to rectify this, a record of colony and microscopic features of 12 selected isolates was performed. The results of preliminary studies indicated that further microbiological and biochemical studies are needed for full characterisation of these organisms. This information is of great importance to bio-prospecting of new Thraustochytrids from Australian ecosystems and would allow for their accurate identification, and so permit the prediction of their PUFA capability by comparison with related genera/species. It was well recognized that environmental stress plays a role in the PUFA production and is mainly due to the reactive oxygen species as abiotic stress (Chiou et al., 2001; Okuyama et al., 2008; Shabala et al., 2009; Shabala et al., 2001). In this aspect, this study makes the first attempt towards better understanding of this phenomenon by way of the use of real-time PCR for the detection of environmental effects on the regulation of PUFA production. Three main environmental conditions including temperature, pH and oxygen availability were monitored as stress inducers. In summary, this study provides novel approaches for the preservation and handling of Thraustochytrids, their molecular biological features, taxonomy, characterisation and responses to environmental factors with respect to their oil production enzymes. The information produced from this study will prove to be vital for both industrial and scientific investigations in the future.

A tissue-engineered humanised xenograft model of human breast cancer-induced bone metastasis and bone colonisation

This thesis focuses on the development of a humanised mouse model to investigate human breast cancer metastasis to bone, an incurable disease presenting a major medical challenge in our society. The method is based on tissue-engineered constructs with human cells that generate a human bone-like organ within mice. This novel platform is further applied to mimic human-specific mechanisms of breast cancer metastasis and growth in human bone, and in particular the role of specific cell adhesion molecules in this process is closely investigated.

Global dissemination of a multidrug resistant Escherichia coli clone

Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant (MDR) clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with several factors, including resistance to fluoroquinolones, high virulence gene content, the possession of the type 1 fimbriae FimH30 allele, and the production of the CTX-M-15 extended spectrum β-lactamase (ESBL). Here, we used genome sequencing to examine the molecular epidemiology of a collection of E. coli ST131 strains isolated from six distinct geographical locations across the world spanning 2000–2011. The global phylogeny of E. coli ST131, determined from whole-genome sequence data, revealed a single lineage of E. coli ST131 distinct from other extraintestinal E. coli strains within the B2 phylogroup. Three closely related E. coli ST131 sublineages were identified, with little association to geographic origin. The majority of single-nucleotide variants associated with each of the sublineages were due to recombination in regions adjacent to mobile genetic elements (MGEs). The most prevalent sublineage of ST131 strains was characterized by fluoroquinolone resistance, and a distinct virulence factor and MGE profile. Four different variants of the CTX-M ESBL–resistance gene were identified in our ST131 strains, with acquisition of CTX-M-15 representing a defining feature of a discrete but geographically dispersed ST131 sublineage. This study confirms the global dispersal of a single E. coli ST131 clone and demonstrates the role of MGEs and recombination in the evolution of this important MDR pathogen.