Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Genetic analysis reveals two stocks of skipjack tuna (Katsuwonus pelamis) in the north western Indian Ocean

Skipjack (SJT) (Katsuwonus pelamis) is a medium sized, pelagic, highly dispersive tuna species that occurs widely across tropical and subtropical waters. SJT constitute the largest tuna fishery in the Indian Ocean, and are currently managed as a single stock. Patterns of genetic variation in a mtDNA gene and 6 microsatellite loci were examined to test for stock structure in the northwestern Indian Ocean. 324 individuals were sampled from five major fishing grounds around Sri Lanka, and single sites in the Maldive Islands and the Laccadive Islands. Phylogenetic reconstruction of mtDNA revealed two coexisting divergent clades in the region. AMOVA (Analysis of Molecular Variance) of mtDNA data revealed significant genetic differentiation among sites (ΦST = 0.2029, P < 0.0001), also supported by SAMOVA results. AMOVA of microsatellite data also showed significant differentiation among most sampled sites (FST = 0.0256, P<0.001) consistent with the mtDNA pattern. STRUCTURE analysis of the microsatellite data revealed two differentiated stocks. While the both two marker types examined identified two genetic groups, microsatellite analysis indicates that the sampled SJT are likely to represent individuals sourced from discrete breeding grounds that are mixed in feeding grounds in Sri Lankan waters.

Evolutionary biology of Gondwanan non-biting midges (Diptera: Chironomidae)

The potential restriction to effective dispersal and gene flow caused by habitat fragmentation can apply to multiple levels of evolutionary scale; from the fragmentation of ancient supercontinents driving diversification and speciation on disjunct landmasses, to the isolation of proximate populations as a result of their inability to cross intervening unsuitable habitat. Investigating the role of habitat fragmentation in driving diversity within and among taxa can thus include inferences of phylogenetic relationships among taxa, assessments of intraspecific phylogeographic structure and analyses of gene flow among neighbouring populations. The proposed Gondwanan clade within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae) represents a model system for investigating the role that population fragmentation and isolation has played at different evolutionary scales. A pilot study by Krosch et al (2009) indentified several highly divergent lineages restricted to ancient rainforest refugia and limited gene flow among proximate sites within a refuge for one member of this clade, Echinocladius martini Cranston. This study provided a framework for investigating the evolutionary history of this taxon and its relatives more thoroughly. Populations of E. martini were sampled in the Paluma bioregion of northeast Queensland to investigate patterns of fine-scale within- and among-stream dispersal and gene flow within a refuge more rigorously. Data was incorporated from Krosch et al (2009) and additional sites were sampled up- and downstream of the original sites. Analyses of genetic structure revealed strong natal site fidelity and high genetic structure among geographically proximate streams. Little evidence was found for regular headwater exchange among upstream sites, but there was distinct evidence for rare adult flight among sites on separate stream reaches. Overall, however, the distribution of shared haplotypes implied that both larval and adult dispersal was largely limited to the natal stream channel. Patterns of regional phylogeographic structure were examined in two related austral orthoclad taxa – Naonella forsythi Boothroyd from New Zealand and Ferringtonia patagonica Sæther and Andersen from southern South America – to provide a comparison with patterns revealed in their close relative E. martini. Both taxa inhabit tectonically active areas of the southern hemisphere that have also experienced several glaciation events throughout the Plio-Pleistocene that are thought to have affected population structure dramatically in many taxa. Four highly divergent lineages estimated to have diverged since the late Miocene were revealed in each taxon, mirroring patterns in E. martini; however, there was no evidence for local geographical endemism, implying substantial range expansion post-diversification. The differences in pattern evident among the three related taxa were suggested to have been influenced by variation in the responses of closed forest habitat to climatic fluctuations during interglacial periods across the three landmasses. Phylogeographic structure in E. martini was resolved at a continental scale by expanding upon the sampling design of Krosch et al (2009) to encompass populations in southeast Queensland, New South Wales and Victoria. Patterns of phylogeographic structure were consistent with expectations and several previously unrecognised lineages were revealed from central- and southern Australia that were geographically endemic to closed forest refugia. Estimated divergence times were congruent with the timing of Plio-Pleistocene rainforest contractions across the east coast of Australia. This suggested that dispersal and gene flow of E. martini among isolated refugia was highly restricted and that this taxon was susceptible to the impacts of habitat change. Broader phylogenetic relationships among taxa considered to be members of this Gondwanan orthoclad group were resolved in order to test expected patterns of evolutionary affinities across the austral continents. The inferred phylogeny and estimated divergence times did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent and implied instead several transoceanic dispersal events post-vicariance. Difficulties in appropriate taxonomic sampling and accurate calibration of molecular phylogenies notwithstanding, the sampling regime implemented in the current study has been the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly has revealed both novel taxa and phylogenetic relationships within and among described genera. Several novel associations between life stages are made here for both described and previously unknown taxa. Investigating evolutionary relationships within and among members of this clade of proposed Gondwanan orthoclad taxa has demonstrated that a complex interaction between historical population fragmentation and dispersal at several levels of evolutionary scale has been important in driving diversification in this group. While interruptions to migration, colonisation and gene flow driven by population fragmentation have clearly contributed to the development and maintenance of much of the diversity present in this group, long-distance dispersal has also played a role in influencing diversification of continental biotas and facilitating gene flow among disjunct populations.

Vulnerability assessment of reinforced concrete columns subjected to vehicular impacts

Columns are one of the key load bearing elements that are highly susceptible to vehicle impacts. The resulting severe damages to columns may leads to failures of the supporting structure that are catastrophic in nature. However, the columns in existing structures are seldom designed for impact due to inadequacies of design guidelines. The impact behaviour of columns designed for gravity loads and actions other than impact is, therefore, of an interest. A comprehensive investigation is conducted on reinforced concrete column with a particular focus on investigating the vulnerability of the exposed columns and to implement mitigation techniques under low to medium velocity car and truck impacts. The investigation is based on non-linear explicit computer simulations of impacted columns followed by a comprehensive validation process. The impact is simulated using force pulses generated from full scale vehicle impact tests. A material model capable of simulating triaxial loading conditions is used in the analyses. Circular columns adequate in capacity for five to twenty story buildings, designed according to Australian standards are considered in the investigation. The crucial parameters associated with the routine column designs and the different load combinations applied at the serviceability stage on the typical columns are considered in detail. Axially loaded columns are examined at the initial stage and the investigation is extended to analyse the impact behaviour under single axis bending and biaxial bending. The impact capacity reduction under varying axial loads is also investigated. Effects of the various load combinations are quantified and residual capacity of the impacted columns based on the status of the damage and mitigation techniques are also presented. In addition, the contribution of the individual parameter to the failure load is scrutinized and analytical equations are developed to identify the critical impulses in terms of the geometrical and material properties of the impacted column. In particular, an innovative technique was developed and introduced to improve the accuracy of the equations where the other techniques are failed due to the shape of the error distribution. Above all, the equations can be used to quantify the critical impulse for three consecutive points (load combinations) located on the interaction diagram for one particular column. Consequently, linear interpolation can be used to quantify the critical impulse for the loading points that are located in-between on the interaction diagram. Having provided a known force and impulse pair for an average impact duration, this method can be extended to assess the vulnerability of columns for a general vehicle population based on an analytical method that can be used to quantify the critical peak forces under different impact durations. Therefore the contribution of this research is not only limited to produce simplified yet rational design guidelines and equations, but also provides a comprehensive solution to quantify the impact capacity while delivering new insight to the scientific community for dealing with impacts.

Designing for engagement towards healthier lifestyles through food image sharing : the case of I8DAT

This paper introduces the underlying design concepts of I8DAT, a food image sharing application that has been developed as part of a three-year research project – Eat, Cook, Grow: Ubiquitous Technology for Sustainable Food Culture in the City (http://www.urbaninformatics .net/projects/food) – exploring urban food practices to engage people in healthier, more environmentally and socially sustainable eating, cooking, and growing food in their everyday lives. The key aim of the project is to produce actionable knowledge, which is then applied to create and test several accessible, user-centred interactive design solutions that motivate user-engagement through playful and social means rather than authoritative information distribution. Through the design and implementation processes we envisage to integrate these design interventions to create a sustainable food network that is both technical and socio-cultural in nature (technosocial). Our primary research locale is Brisbane, Australia, with additional work carried out in three reference cities with divergent geographic, socio-cultural, and technological backgrounds: Seoul, South Korea, for its global leadership in ubiquitous technology, broadband access, and high population density; Lincoln, UK, for the regional and peri-urban dimension it provides, and Portland, Oregon, US, for its international standing as a hub of the sustainable food movement.

The 2008 Tibet riots : perspectives, divided group protests and divergent media narratives

Awareness of the power of the mass media to communicate images of protest to global audiences and, in so doing, to capture space in global media discourses is a central feature of the transnational protest movement. A number of protest movements have formed around opposition to concepts and practices that operate beyond national borders, such as neoliberal globalization or threats to the environment. However, transnational protests also involve more geographically discreet issues such as claims to national independence or greater religious or political freedom by groups within specific national contexts. Appealing to the international community for support is a familiar strategy for communities who feel that they are being discriminated against or ignored by a national government.

Measurement and correlates of caregiver self-efficacy amongst family caregivers of persons with dementia living in Shanghai, China

Background: Caring for family members with dementia can be a long-term, burdensome task resulting in physical and emotional distress and impairment. Research has demonstrated significantly lower levels of selfefficacy among family caregivers of people with dementia (CGs) than caregivers of relatives with non-dementia diseases. Intervention studies have also suggested that the mental and physical health of dementia CGs could be improved through the enhancement of their self-efficacy. However, studies are limited in terms of the influences of caregiver self-efficacy on caregiver behaviour, subjective burden and health-related quality of life. Of particular note is that there are no studies on the applicability of caregiver self-efficacy in the social context of China. Objective: The purpose of this thesis was to undertake theoretical exploration using Bandura’s (1997) self-efficacy theory to 1) revise the Revised Caregiving Self-Efficacy Scale (C-RCSES) (Steffen, McKibbin, Zeiss, Gallagher-Thompson, & Bandura, 2002), and 2) explore determinants of caregiver self-efficacy and the role of caregiver self-efficacy and other conceptual constructs (including CGs’ socio-demographic characteristics, CRs’ impairment and CGs’ social support) in explaining and predicting caregiver behaviour, subjective burden and health-related quality of life among CGs in China. Methodology: Two studies were undertaken: a qualitative elicitation study with 10 CGs; and a cross-sectional survey with 196 CGs. In the first study, semi-structured interviews were conducted to explore caregiver behaviours and corresponding challenges for their performance. The findings of the study assisted in the development of the initial items and domains of the Chinese version of the Revised Caregiving Self-Efficacy Scale (C-RCSES). Following changes to items in the scale, the second study, a cross-sectional survey with 196 CGs was conducted to evaluate the psychometric properties of C-RCSES and to test a hypothesised self-efficacy model of family caregiving adapted from Bandura’s theory (1997). Results: 35 items were generated from the qualitative data. The content validity of the C-RCSES was assessed and ensured in Study One before being used for the cross-sectional survey. Eight items were removed and five subscales (caregiver self-efficacy for gathering information about treatment, symptoms and health care; obtaining support; responding to problematic behaviours; management of household, personal and medical care; and controlling upsetting thoughts about caregiving) were identified after principal component factor analysis on the cross-sectional survey data. The reliability of the scale is acceptable: the Cronbach’s alpha coefficients for the whole scale and for each subscale were all over .80; and the fourweek test-retest reliabilities for the whole scale and for each subscale ranged from .64 to .85. The concurrent, convergent and divergent validity were also acceptable. CGs reported moderate levels of caregiver self-efficacy. Furthermore, the level of self-efficacy for management of household, personal and medical care was relatively high in comparison to those of the other four domains of caregiver self-efficacy. Caregiver self-efficacy was also significantly influenced by CGs’ socio-demographic characteristics and the caregiving external factors (CR impairment and social support that CGs obtained). The level of caregiver behaviour that CGs reported was higher than that reported in other Chinese research. CGs’ socio-demographics significantly influenced caregiver behaviour, whereas caregiver self-efficacy did not influence caregiver behaviour. Regarding the two external factors, CGs who cared for highly impaired relatives reported high levels of caregiver behaviour, but social support did not influence caregiver behaviour. Regarding caregiver subjective burden and health-related quality of life, CGs reported moderate levels of subjective burden, and their level of healthrelated quality of life was significantly lower than that of the general population in China. The findings also indicated that CGs’ subjective burden and health-related quality of life were influenced by all major factors in the hypothesised model, including CGs’ socio-demographics, CRs’ impairment, social support that CGs obtained, caregiver self-efficacy and caregiver behaviour. Of these factors, caregiver self-efficacy and social support significantly improved their subjective burden and health-related quality of life; whereas caregiver behaviour and CRs’ impairment were detrimental to CGs, such as increasing subjective burden and worsening health-related quality of life. Conclusion: While requiring further exploration, the qualitative study was the first qualitative research conducted in China to provide an in-depth understanding of CGs’ caregiving experience, including their major caregiver behaviours and the corresponding challenges. Meanwhile, although the C-RCSES needs further psychometric testing, it is a useful tool for assessing caregiver self-efficacy in Chinese populations. Results of the qualitative and quantitative study provide useful information for future studies regarding the explanatory power of caregiver self-efficacy to caregiver behaviour, subjective burden and health-related quality of life. Additionally, integrated with Bandura’s theory, the findings from the quantitative study also suggested a further study exploring the role of outcome expectations in caregiver behaviour, subjective burden and healthrelated quality of life.

Early signaling responses to divergent exercise stimuli in skeletal muscle from well-trained humans

Skeletal muscle from strength- and endurance-trained individuals represents diverse adaptive states. In this regard, AMPK-PGC-1α signaling mediates several adaptations to endurance training, while up-regulation of the Akt-TSC2-mTOR pathway may underlie increased protein synthesis after resistance exercise. We determined the effect of prior training history on signaling responses in seven strength-trained and six endurance-trained males who undertook 1 h cycling at 70% VO2peak or eight sets of five maximal repetitions of isokinetic leg extensions. Muscle biopsies were taken at rest, immediately and 3 h postexercise. AMPK phosphorylation increased after cycling in strength-trained (54%; P<0.05) but not endurance-trained subjects. Conversely, AMPK was elevated after resistance exercise in endurance- (114%; P<0.05), but not strengthtrained subjects. Akt phosphorylation increased in endurance- (50%; P<0.05), but not strengthtrained subjects after cycling but was unchanged in either group after resistance exercise. TSC2 phosphorylation was decreased (47%; P<0.05) in endurance-trained subjects following resistance exercise, but cycling had little effect on the phosphorylation state of this protein in either group. p70S6K phosphorylation increased in endurance- (118%; P<0.05), but not strength-trained subjects after resistance exercise, but was similar to rest in both groups after cycling. Similarly, phosphorylation of S6 protein, a substrate for p70 S6K, was increased immediately following resistance exercise in endurance- (129%; P<0.05), but not strength-trained subjects. In conclusion, a degree of “response plasticity” is conserved at opposite ends of the endurancehypertrophic adaptation continuum. Moreover, prior training attenuates the exercise specific signaling responses involved in single mode adaptations to training.

Machine recognition of hand-drawn circuit diagrams

An application of image processing techniques to recognition of hand-drawn circuit diagrams is presented. The scanned image of a diagram is pre-processed to remove noise and converted to bilevel. Morphological operations are applied to obtain a clean, connected representation using thinned lines. The diagram comprises of nodes, connections and components. Nodes and components are segmented using appropriate thresholds on a spatially varying object pixel density. Connection paths are traced using a pixel-stack. Nodes are classified using syntactic analysis. Components are classified using a combination of invariant moments, scalar pixel-distribution features, and vector relationships between straight lines in polygonal representations. A node recognition accuracy of 82% and a component recognition accuracy of 86% was achieved on a database comprising 107 nodes and 449 components. This recogniser can be used for layout “beautification” or to generate input code for circuit analysis and simulation packages

The current context of Queensland primary teacher engagement with professional learning through professional associations

Engaging Queensland primary teachers in professional associations can be a challenge, particularly for subject-specific associations. Professional associations are recognised providers of professional learning. By not being involved in professional associations primary teachers are missing potential quality professional learning opportunities that can impact the results of their students. The purpose of the research is twofold: Firstly, to provide a thorough understanding of the current context in order to assist professional associations who wish to change from their current level of primary teacher engagement; and secondly, to contribute to the literature in the area of professional learning for primary teachers within professional associations. Using a three part research design, interviews of primary teachers and focus groups of professional association participants and executives were conducted and themed to examine the current context of engagement. Force field analysis was used to provide the framework to identify the driving and restraining forces for primary teacher engagement in professional learning through professional associations. Communities of practice and professional learning communities were specifically examined as potential models for professional associations to consider. The outcome is a diagrammatic framework outlining the current context of primary teacher engagement, specifically the driving and restraining forces of primary teacher engagement with professional associations. This research also identifies considerations for professional associations wishing to change their level of primary teacher engagement. The results of this research show that there are key themes that provide maximum impact if wishing to increase engagement of primary teachers in professional associations. However the implications of this lies with professional associations and their alignment between intent and practice dedicated to this change.

Population genetic structure and patterns of dispersal in the Giant Long-Armed Prawn, Macrobrachium lar (Fabricius, 1798) (Decapoda : Palaemonidae)

The Giant Long-Armed Prawn, Macrobrachium lar is a freshwater species native to the Indo-Pacific. M. lar has a long-lived, passive, pelagic marine larval stage where larvae need to colonise freshwater within three months to complete their development. Dispersal is likely to be influenced by the extensive distances larvae must transit between small oceanic islands to find suitable freshwater habitat, and by prevailing east to west wind and ocean currents in the southern Pacific Ocean. Thus, both intrinsic and extrinsic factors are likely to influence wild population structure in this species. The present study sought to define the contemporary broad and fine-scale population genetic structure of Macrobrachium lar in the south-western Pacific Ocean. Three polymorphic microsatellite loci were used to assess patterns of genetic variation within and among 19 wild adult sample sites. Statistical procedures that partition variation implied that at both spatial scales, essentially all variation was present within sample sites and differentiation among sites was low. Any differentiation observed also was not correlated with geographical distance. Statistical approaches that measure genetic distance, at the broad-scale, showed that all south-western Pacific Islands were essentially homogeneous, with the exception of a well supported divergent Cook Islands group. These findings are likely the result of some combination of factors that may include the potential for allelic homoplasy, through to the effects of sampling regime. Based on the findings, there is most likely a divergent M. lar Cook Islands clade in the south-western Pacific Ocean, resulting from prevailing ocean currents. Confirmation of this pattern will require a more detailed analysis of nDNA variation using a larger number of loci and, where possible, use of larger population sizes.

Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.

A phenomenological model for the structure-composition relationship of the high Tc cuprates based on simple chemical principles

A simple phenomenological model for the relationship between structure and composition of the high Tc cuprates is presented. The model is based on two simple crystal chemistry principles: unit cell doping and charge balance within unit cells. These principles are inspired by key experimental observations of how the materials accommodate large deviations from stoichiometry. Consistent explanations for significant HTSC properties can be explained without any additional assumptions while retaining valuable insight for geometric interpretation. Combining these two chemical principles with a review of Crystal Field Theory (CFT) or Ligand Field Theory (LFT), it becomes clear that the two oxidation states in the conduction planes (typically d8 and d9) belong to the most strongly divergent d-levels as a function of deformation from regular octahedral coordination. This observation offers a link to a range of coupling effects relating vibrations and spin waves through application of Hund’s rules. An indication of this model’s capacity to predict physical properties for HTSC is provided and will be elaborated in subsequent publications. Simple criteria for the relationship between structure and composition in HTSC systems may guide chemical syntheses within new material systems.