Purine Nucleoside Phosphorylase mediated molecular chemotherapy and conventional chemotherapy: A tangible union against chemoresistant cancer

Background Late stage Ovarian Cancer is essentially incurable primarily due to late diagnosis and its inherent heterogeneity. Single agent treatments are inadequate and generally lead to severe side effects at therapeutic doses. It is crucial to develop clinically relevant novel combination regimens involving synergistic modalities that target a wider repertoire of cells and lead to lowered individual doses. Stemming from this premise, this is the first report of two- and three-way synergies between Adenovirus-mediated Purine Nucleoside Phosphorylase based gene directed enzyme prodrug therapy (PNP-GDEPT), docetaxel and/or carboplatin in multidrug-resistant ovarian cancer cells. Methods The effects of PNP-GDEPT on different cellular processes were determined using Shotgun Proteomics analyses. The in vitro cell growth inhibition in differentially treated drug resistant human ovarian cancer cell lines was established using a cell-viability assay. The extent of synergy, additivity, or antagonism between treatments was evaluated using CalcuSyn statistical analyses. The involvement of apoptosis and implicated proteins in effects of different treatments was established using flow cytometry based detection of M30 (an early marker of apoptosis), cell cycle analyses and finally western blot based analyses. Results Efficacy of the trimodal treatment was significantly greater than that achieved with bimodal- or individual treatments with potential for 10-50 fold dose reduction compared to that required for individual treatments. Of note was the marked enhancement in apoptosis that specifically accompanied the combinations that included PNP-GDEPT and accordingly correlated with a shift in the expression of anti- and pro-apoptotic proteins. PNP-GDEPT mediated enhancement of apoptosis was reinforced by cell cycle analyses. Proteomic analyses of PNP-GDEPT treated cells indicated a dowregulation of proteins involved in oncogenesis or cancer drug resistance in treated cells with accompanying upregulation of apoptotic- and tumour- suppressor proteins. Conclusion Inclusion of PNP-GDEPT in regular chemotherapy regimens can lead to significant enhancement of the cancer cell susceptibility to the combined treatment. Overall, these data will underpin the development of regimens that can benefit patients with late stage ovarian cancer leading to significantly improved efficacy and increased quality of life.

Molecular structure of the mineral svanbergite SrAl3(PO 4,SO4)2(OH)6 - A vibrational spectroscopic study

The mineral svanbergite SrAl 3(PO 4,SO 4) 2(OH) 6 is a hydroxy phosphate-sulphate mineral belonging to the beudantite subgroup of alunites and has been characterised by vibrational spectroscopy. Bands at various wavenumbers were assigned to the different vibrational modes of svanbergite, which were then associated with the structure of the mineral. Bands were primarily assigned to phosphate and sulphate stretching and bending modes. Two symmetric stretching modes for both phosphate and sulphate supported the concept of non-equivalent phosphate and sulphate units in the mineral structure. Bands in the OH stretching region enabled hydrogen bond distances to be calculated. Comparison of the hydrogen bond distances and the calculated hydrogen bond distances from the structure models indicates that hydrogen bonding in svanbergite occurs between the two OH units rather than OH to SO42- units.

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.

Molecular characterisation of environmental enterococci derived from water samples and assessment of associated public health hazards

Enterococci are versatile Gram-positive bacteria that can survive under extreme conditions. Most enterococci are non-virulent and found in the gastrointestinal tract of humans and animals. Other strains are opportunistic pathogens that contribute to a large number of nosocomial infections globally. Epidemiological studies demonstrated a direct relationship between the density of enterococci in surface waters and the risk of swimmer-associated gastroenteritis. The distribution of infectious enterococcal strains from the hospital environment or other sources to environmental water bodies through sewage discharge or other means, could increase the prevalence of these strains in the human population. Environmental water quality studies may benefit from focusing on a subset of Enterococcus spp. that are consistently associated with sources of faecal pollution such as domestic sewage, rather than testing for the entire genus. E. faecalis and E. faecium are potentially good focal species for such studies, as they have been consistently identified as the dominant Enterococcus spp. in human faeces and sewage. On the other hand enterococcal infections are predominantly caused by E. faecalis and E. faecium. The characterisation of E. faecalis and E. faecium is important in studying their population structures, particularly in environmental samples. In developing and implementing rapid, robust molecular genotyping techniques, it is possible to more accurately establish the relationship between human and environmental enterococci. Of particular importance, is to determine the distribution of high risk enterococcal clonal complexes, such as E. faecium clonal complex 17 and E. faecalis clonal complexes 2 and 9 in recreational waters. These clonal complexes are recognized as particularly pathogenic enterococcal genotypes that cause severe disease in humans globally. The Pimpama-Coomera watershed is located in South East Queensland, Australia and was investigated in this study mainly because it is used intensively for agriculture and recreational purposes and has a strong anthropogenic impact. The primary aim of this study was to develop novel, universally applicable, robust, rapid and cost effective genotyping methods which are likely to yield more definitive results for the routine monitoring of E. faecalis and E. faecium, particularly in environmental water sources. To fullfill this aim, new genotyping methods were developed based on the interrogation of highly informative single nucleotide polymorphisms (SNPs) located in housekeeping genes of both E. faecalis and E. faecium. SNP genotyping was successfully applied in field investigations of the Coomera watershed, South-East Queensland, Australia. E. faecalis and E. faecium isolates were grouped into 29 and 23 SNP profiles respectively. This study showed the high longitudinal diversity of E. faecalis and E. faecium over a period of two years, and both human-related and human-specific SNP profiles were identified. Furthermore, 4.25% of E. faecium strains isolated from water was found to correspond to the important clonal complex-17 (CC17). Strains that belong to CC17 cause the majority of hospital outbreaks and clinical infections globally. Of the six sampling sites of the Coomera River, Paradise Point had the highest number of human-related and human-specific E. faecalis and E. faecium SNP profiles. The secondary aim of this study was to determine the antibiotic-resistance profiles and virulence traits associated with environmental E. faecalis and E. faecium isolates compared to human pathogenic E. faecalis and E. faecium isolates. This was performed to predict the potential health risks associated with coming into contact with these strains in the Coomera watershed. In general, clinical isolates were found to be more resistant to all the antibiotics tested compared to water isolates and they harbored more virulence traits. Multi-drug resistance was more prevalent in clinical isolates (71.18% of E. faecalis and 70.3 % of E. faecium) compared to water isolates (only 5.66 % E. faecium). However, tetracycline, gentamicin, ciprofloxacin and ampicillin resistance was observed in water isolates. The virulence gene esp was the most prevalent virulence determinant observed in clinical isolates (67.79% of E. faecalis and 70.37 % of E. faecium), and this gene has been described as a human-specific marker used for microbial source tracking (MST). The presence of esp in water isolates (16.36% of E. faecalis and 19.14% of E. faecium) could be indicative of human faecal contamination in these waterways. Finally, in order to compare overall gene expression between environmental and clinical strains of E. faecalis, a comparative gene hybridization study was performed. The results of this investigation clearly demonstrated the up-regulation of genes associated with pathogenicity in E. faecalis isolated from water. The expression study was performed at physiological temperatures relative to ambient temperatures. The up-regulation of virulence genes demonstrates that environmental strains of E. faecalis can pose an increased health risk which can lead to serious disease, particularly if these strains belong to the virulent CC17 group. The genotyping techniques developed in this study not only provide a rapid, robust and highly discriminatory tool to characterize E. faecalis and E. faecium, but also enables the efficient identification of virulent enterococci that are distributed in environmental water sources.

A molecular phylogeny for the Tribe Dacini (Diptera: Tephritidae) : systematic and biogeographic implications

With well over 700 species, the Tribe Dacini is one of the most species-rich clades within the dipteran family Tephritidae, the true fruit flies. Nearly all Dacini belong to one of two very large genera, Dacus Fabricius and Bactrocera Macquart. The distribution of the genera overlap in or around the Indian subcontinent, but the greatest diversity of Dacus is in Africa and the greatest diversity of Bactrocera is in south-east Asia and the Pacific. The monophyly of these two genera has not been rigorously established, with previous phylogenies only including a small number of species and always heavily biased to one genus over the other. Moreover, the subgeneric taxonomy within both genera is complex and the monophyly of many subgenera has not been explicitly tested. Previous hypotheses about the biogeography of the Dacini based on morphological reviews and current distributions of taxa have invoked an out-of-India hypothesis; however this has not been tested in a phylogenetic framework. We attempted to resolve these issues with a dated, molecular phylogeny of 125 Dacini species generated using 16S, COI, COII and white eye genes. The phylogeny shows that Bactrocera is not monophyletic, but rather consists of two major clades: Bactrocera s.s. and the ‘Zeugodacus group of subgenera’ (a recognised, but informal taxonomic grouping of 15 Bactrocera subgenera). This ‘Zeugodacus’ clade is the sister group to Dacus, not Bactrocera and, based on current distributions, split from Dacus before that genus moved into Africa. We recommend that taxonomic consideration be given to raising Zeugodacus to genus level. Supportive of predictions following from the out-of-India hypothesis, the first common ancestor of the Dacini arose in the mid-Cretaceous approximately 80 mya. Major divergence events occurred during the Indian rafting period and diversification of Bactrocera apparently did not begin until after India docked with Eurasia (50–35 mya). In contrast, diversification in Dacus, at approximately 65 mya, apparently began much earlier than predicted by the out-of-India hypothesis, suggesting that, if the Dacini arose on the Indian plate, then ancestral Dacus may have left the plate in the mid to late Cretaceous via the well documented India–Madagascar–Africa migration route. We conclude that the phylogeny does not disprove the predictions of an out-of-India hypothesis for the Dacini, although modification of the original hypothesis is required.

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae) : robust support for interfamilial relationships and molecular synapomorphies define major clades

Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites + Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus + termites), and a further series of compensatory base changes in this stem loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae + Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae.

Supramolecular selection in molecular alloys

Complexes of the type \[M(phen)3](PF6)2 (M = Ni(II), Fe(II), Ru(II) and phen = 1,10-phenanthroline) were found to co-crystallize to form molecular alloys (solid solutions of molecules) with general formula \[MAxMB1–x(phen)3](PF6)2·0.5H2O in which the relative concentrations of the metal complexes in the crystals closely match those in the crystallizing solution. Consequently, the composition of the co-crystals can be accurately predicted and controlled by modulating the relative concentrations of the metal complexes in the crystallizing solution. Although they are chemically and structurally similar, complexes of the type \[M(bipy)3](PF6)2 (M = Ni(II), Fe(II), Ru(II) and bipy = 2,2′-bipyridine) display markedly different behavior upon co-crystallization. In this case, the resulting co-crystals of general formula \[MAxMB1–x(bipy)3](PF6)2 have relative concentrations of the constituent complexes that are markedly different from the relative concentrations of the complexes initially present in the crystallizing solution. For example, when the nickel and iron complexes are co-crystallized from a solution containing a 50:50 ratio of each, the result is the formation of some crystals with a higher proportion of iron and others with a higher proportion of nickel. The relative concentrations of the metal complexes in the crystals can vary from those in the crystallizing solutions by as much as 15%. This result was observed for a range of combinations of metal complexes (Ni/Fe, Ni/Ru, and Fe/Ru) and a range of starting concentrations in the crystallizing solutions (90:10 through to 10:90 in 10% increments). To explain this remarkable result, we introduce the concept of “supramolecular selection”, which is a process driven by molecular recognition that leads to the partially selective aggregation of like molecules during crystallization.

Beyond barcoding : a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.

The governance of inter-organisational decision-making : understanding the impacts of informal networks on formal decision-making regimes in the Brisbane Airport region

Airports and cities inevitably recognise the value that each brings the other; however, the separation in decision-making authority for what to build, where, when and how provides a conundrum for both parties. Airports often want a say in what is developed outside of the airport fence, and cities often want a say in what is developed inside the airport fence. Defining how much of a say airports and cities have in decisions beyond their jurisdictional control is likely to be a topic that continues so long as airports and cities maintain separate formal decision-making processes for what to build, where, when and how. However, the recent Green and White Papers for a new National Aviation Policy have made early inroads to formalising relationships between Australia’s major airports and their host cities. At present, no clear indication (within practice or literature) is evident to the appropriateness of different governance arrangements for decisions to develop in situations that bring together the opposing strategic interests of airports and cities; thus leaving decisions for infrastructure development as complex decision-making spaces that hold airport and city/regional interests at stake. The line of enquiry is motivated by a lack of empirical research on networked decision-making domains outside of the realm of institutional theorists (Agranoff & McGuire, 2001; Provan, Fish & Sydow, 2007). That is, governance literature has remained focused towards abstract conceptualisations of organisation, without focusing on the minutia of how organisation influences action in real-world applications. A recent study by Black (2008) has provided an initial foothold for governance researchers into networked decision-making domains. This study builds upon Black’s (2008) work by aiming to explore and understand the problem space of making decisions subjected to complex jurisdictional and relational interdependencies. That is, the research examines the formal and informal structures, relationships, and forums that operationalise debates and interactions between decision-making actors as they vie for influence over deciding what to build, where, when and how in airport-proximal development projects. The research mobilises a mixture of qualitative and quantitative methods to examine three embedded cases of airport-proximal development from a network governance perspective. Findings from the research provide a new understanding to the ways in which informal actor networks underpin and combine with formal decision-making networks to create new (or realigned) governance spaces that facilitate decision-making during complex phases of development planning. The research is timely, and responds well to Isett, Mergel, LeRoux, Mischen and Rethemeyer’s (2011) recent critique of limitations within current network governance literature, specifically to their noted absence of empirical studies that acknowledge and interrogate the simultaneity of formal and informal network structures within network governance arrangements (Isett et al., 2011, pp. 162-166). The combination of social network analysis (SNA) techniques and thematic enquiry has enabled findings to document and interpret the ways in which decision-making actors organise to overcome complex problems for planning infrastructure. An innovative approach to using association networks has been used to provide insights to the importance of the different ways actors interact with one another, thus providing a simple yet valuable addition to the increasingly popular discipline of SNA. The research also identifies when and how different types of networks (i.e. formal and informal) are able to overcome currently known limitations to network governance (see McGuire & Agranoff, 2011), thus adding depth to the emerging body of network governance literature surrounding limitations to network ways of working (i.e. Rhodes, 1997a; Keast & Brown, 2002; Rethemeyer & Hatmaker, 2008; McGuire & Agranoff, 2011). Contributions are made to practice via the provision of a timely understanding of how horizontal fora between airports and their regions are used, particularly in the context of how they reframe the governance of decision-making for airport-proximal infrastructure development. This new understanding will enable government and industry actors to better understand the structural impacts of governance arrangements before they design or adopt them, particularly for factors such as efficiency of information, oversight, and responsiveness to change.

Molecular dynamics studies of the effects of branching characteristics on the crystalline structure of polyethylene

Molecular dynamics simulations were carried out on single chain models of linear low-density polyethylene in vacuum to study the effects of branch length, branch content, and branch distribution on the polymer’s crystalline structure at 300 K. The trans/gauche (t/g) ratios of the backbones of the modeled molecules were calculated and utilized to characterize their degree of crystallinity. The results show that the t/g ratio decreases with increasing branch content regardless of branch length and branch distribution, indicating that branch content is the key molecular parameter that controls the degree of crystallinity. Although t/g ratios of the models with the same branch content vary, they are of secondary importance. However, our data suggests that branch distribution (regular or random) has a significant effect on the degree of crystallinity for models containing 10 hexyl branches/1,000 backbone carbons. The fractions of branches that resided in the equilibrium crystalline structures of the models were also calculated. On average, 9.8% and 2.5% of the branches were found in the crystallites of the molecules with ethyl and hexyl branches while C13 NMR experiments showed that the respective probabilities of branch inclusion for ethyl and hexyl branches are 10% and 6% [Hosoda et al., Polymer 1990, 31, 1999–2005]. However, the degree of branch inclusion seems to be insensitive to the branch content and branch distribution.