Effects of dissolved oxygen availability and culture biomass at induction upon the intracellular expression of monoamine oxidase by recombinant E. coli in fed batch bioprocesses

The effects of oxygen availability and induction culture biomass upon production of an industrially important monoamine oxidase (MAO) were investigated in fed-batch cultures of a recombinant E. coli. For each induction cell biomass 2 different oxygenation methods were used, aeration and oxygen enriched air. Induction at higher biomass levels increased the culture demand for oxygen, leading to fermentative metabolism and accumulation of high levels of acetate in the aerated cultures. Paradoxically, despite an almost eight fold increase in acetate accumulation to levels widely reported to be highly detrimental to protein production, when induction wet cell weight (WCW) rose from 100% to 137.5%, MAO specific activity in these aerated processes showed a 3 fold increase. By contrast, for oxygenated cultures induced at WCW's 100% and 137.5% specific activity levels were broadly similar, but fell rapidly after the maxima were reached. Induction at high biomass levels (WCW 175%) led to very low levels of specific MAO activity relative to induction at lower WCW's in both aerated and oxygenated cultures. Oxygen enrichment of these cultures was a useful strategy for boosting specific growth rates, but did not have positive effects upon specific enzyme activity. Based upon our findings, consideration of the amino acid composition of MAO and previous studies on related enzymes, we propose that this effect is due to oxidative damage to the MAO enzyme itself during these highly aerobic processes. Thus, the optimal process for MAO production is aerated, not oxygenated, and induced at moderate cell density, and clearly represents a compromise between oxygen supply effects on specific growth rate/induction cell density, acetate accumulation, and high specific MAO activity. This work shows that the negative effects of oxygen previously reported in free enzyme preparations, are not limited to these acellular environments but are also discernible in the sheltered environment of the cytosol of E. coli cells.

Burden of non-communicable diseases (NCDs) in Nepal and the availability and affordability of NCD medicines

Background: Traditionally communicable diseases were the main causes of burden in developing countries like Nepal. In recent years non-communicable diseases (NCDs), mainly cardiovascular diseases (CVDs), cancer, chronic respiratory diseases and diabetes mellitus, impose a larger disease burden compared to communicable diseases. Most elements of health and medicine policies in Nepal are still focused on communicable diseases. There is limited evidence about NCDs and NCD medicines in Nepal. Aim: To explore the gap between the burden of NCDs and the availability and affordability of NCD medicines in Nepal. Methods: Biomedical databases like Medline, Scopus, Web of Science and other online sources (including Global Burden of Diseases data) were searched for data on the burden of NCDs in term of Disability Adjusted Life Years (DALYs). The Essential Medicines List (EML) of Nepal was compared with World Health Organisation (EML) for inclusion of NCD medicines. Results: In Nepal, NCDs caused nearly 45% of the total 10.5 million DALYs in 2010. CVDs (15.2%), were the leading cause of NCDs burden followed by chronic respiratory diseases (14.7%), cancer (7.3%) and diabetes mellitus (3.2%). One hospital based national survey found that 37% of hospitalised patients had NCDs. Among them, 38% had heart disease followed by COPD (33%) , and diabetes (10%). Most (23 out of 28) non-cancer NCD medicines recommended in WHO-EML were present in Nepal's EML, theoretically indicating good availability. However, it is difficult to say whether they are accessible and affordable due to the lack of adequate data on access and pricing. Conclusion: This study gives some insight into the burden of NCDs. Although NCD medicines are available in Nepal, further research is required to determine whether they are accessible and affordable to the general population.

Evolution to a chronic disease niche correlates with increased sensitivity to tryptophan availability for the obligate intracellular bacterium Chlamydia pneumoniae

The chlamydiae are obligate intracellular parasites that have evolved specific interactions with their various hosts and host cell types to ensure their successful survival and consequential pathogenesis. The species Chlamydia pneumoniae is ubiquitous, with serological studies showing that most humans are infected at some stage in their lifetime. While most human infections are asymptomatic, C. pneumoniae can cause more-severe respiratory disease and pneumonia and has been linked to chronic diseases such as asthma, atherosclerosis, and even Alzheimer's disease. The widely dispersed animal-adapted C. pneumoniae strains cause an equally wide range of diseases in their hosts. It is emerging that the ability of C. pneumoniae to survive inside its target cells, including evasion of the host's immune attack mechanisms, is linked to the acquisition of key metabolites. Tryptophan and arginine are key checkpoint compounds in this host-parasite battle. Interestingly, the animal strains of C. pneumoniae have a slightly larger genome, enabling them to cope better with metabolite restrictions. It therefore appears that as the evolutionarily more ancient animal strains have evolved to infect humans, they have selectively become more "susceptible" to the levels of key metabolites, such as tryptophan. While this might initially appear to be a weakness, it allows these human C. pneumoniae strains to exquisitely sense host immune attack and respond by rapidly reverting to a persistent phase. During persistence, they reduce their metabolic levels, halting progression of their developmental cycle, waiting until the hostile external conditions have passed before they reemerge.

Diverse urban plantings managed with sufficient resource availability can increase plant productivity and arthropod diversity

Buildings structures and surfaces are explicitly being used to grow plants, and these “urban plantings” are generally designed for aesthetic value. Urban plantings also have the potential to contribute significant “ecological values” by increasing urban habitat for animals such as arthropods and by increasing plant productivity. In this study, we evaluated how the provision of these additional ecological values is affected by plant species richness; the availability of essential resources for plants, such as water, light, space; and soil characteristics. We sampled 33 plantings located on the exterior of three buildings in the urban center of Brisbane, Australia (subtropical climatic region) over 2, 6 week sampling periods characterized by different temperature and rainfall conditions. Plant cover was estimated as a surrogate for productivity as destructive sampling of biomass was not possible. We measured weekly light levels (photosynthetically active radiation), plant CO2 assimilation, soil CO2 efflux, and arthropod diversity. Differences in plant cover were best explained by a three-way interaction of plant species richness, management water regime and sampling period. As the richness of plant species increased in a planter, productivity and total arthropod richness also increased significantly—likely due to greater habitat heterogeneity and quality. Overall we found urban plantings can provide additional ecological values if essential resources are maintained within a planter such as water, light and soil temperature. Diverse urban plantings that are managed with these principles in mind can contribute to the attraction of diverse arthropod communities, and lead to increased plant productivity within a dense urban context.

The potential availability of roosting sites for lesser short-tailed bats (Mystacina tuberculata) on Kapiti Island, New Zealand: Implications for a translocation

Lesser short-tailed bats (Mystacina tuberculata) have recently been translocated to Kapiti Island in an attempt to form a new population of this threatened species. However, the island's vegetation is regenerating, and there was doubt that the forests provided enough large trees with cavities for bats to roost in. This study measured the availability of tree-trunk cavities of the right size for potential roost sites on Kapiti Island, and assessed if habitat restoration would be required to increase the translocation's chance of success. First, trees with cavities accessible to us were sampled in six of Kapiti Island's forest types. Size variables known to affect roost site selection by lesser short-tailed bats at the tree and cavity level were measured. Trees were classified as containing cavities that could potentially provide suitable roosts if their values for all variables measured fell within the range of roosts used by lesser short-tailed bats in natural populations. Roosts were classified as suitably sized for solitary bats or for colonies, using measurements from both types of roosts in natural populations. Second, the density of these potential roost cavities was calculated. Cavities of a size potentially suitable for colonies were found in four of the six forest types at densities ranging from 3.2 +/- 3.2 SE to 52.4 +/- 14.0 trees per ha. Density of potential solitary roosts was much higher. Not all potential cavities will be suitable because they may be damp, poorly insulated, or have an unsuitable microclimate. Nevertheless, our estimates indicated that the two most extensive forest types each contained thousands of potential cavities of a size suitable for colonies of lesser short-tailed bats. In addition, there were tens of thousands of cavities large enough to shelter solitary bats. Roost habitat restoration appears unnecessary to assist translocated Mystacina tuberculata on Kapiti Island.

Measuring the regional availability of biomass for biofuels and the potential for microalgae

Biomass is an important energy resource for producing bioenergy and growing the global economy whilst minimising greenhouse gas emissions. Many countries, like Australia have a huge amount of biomass with the potential for bioenergy, but non-edible feedstock resources are significantly under-exploited. Hence it is essential to map the availability of these feedstocks to identify the most appropriate bioenergy solution for each region and develop supply chains for biorefineries. Using Australia as a case study,we present the spatial availability and opportunities for second and third generation feedstocks. Considerations included current land use, the presence of existing biomass industries and climatic conditions. Detailed information on the regional availability of biomass was collected from government statistics, technical reports and energy assessments as well as from academic literature. Second generation biofuels have the largest opportunity in New South Wales, Queensland and Victoria (NSW, QLD and VIC) and the regions with the highest potential for microalgae are Western Australia and Northern Territory (WA, NT), based on land use opportunity cost and climate. The approach can be used in other countries with a similar climate. More research is needed to overcome key technical and economic hurdles.

Raman spectroscopy of some complex arsenate minerals—implications for soil remediation

The application of spectroscopy to the study of contaminants in soils is important. Among the many contaminants is arsenic, which is highly labile and may leach to non-contaminated areas. Minerals of arsenate may form depending upon the availability of specific cations for example calcium and iron. Such minerals include carminite, pharmacosiderite and talmessite. Each of these arsenate minerals can be identified by its characteristic Raman spectrum enabling identification.

A New Opportunity to Pulp Bagasse in Australia?

Despite the large quantity of sugarcane grown in Australia, no bagasse is pulped in the country. This is largely because of an established pulp industry based on the abundant native hardwood resources. However, increasing demand for fibre and the limited availability of additional forest areas make bagasse pulping attractive. Issues relating to infrastructure and economics are discussed, and scenarios of acceptable risk identified. It is shown that there should be scope for the production of bleached bagasse pulp in Australia.

i-Cobb - An innovative technique in spinal radiographic measurement

The measurement of Cobb angles from radiographs is routine practice in spinal clinics. The technique relies on the use and availability of specialist equipment such as a goniometer, cobbometer or protractor. The aim of this study was to validate the use of i-Phone (Apple Inc) combined with Tilt Meter Pro software as compared to a protractor in the measurement of Cobb angles. Between November 2008 and December 2008 20 patients were selected at random from the Paediatric Spine Research Groups Database. A power calculation was performed which indicated if n=240 measurements the study had a 96% chance of detecting a 5 degree difference between groups. All patients had idiopathic scoliosis with a range of curve types and severities. The study found the i-Phone combined with Tilt Meter Pro software offers a faster alternative to the traditional method of Cobb angle measurement. The use of i-Phone offers a more convenient way of measuring Cobb angles in the outpatient setting. The intra-observer repeatability of the iPhone is equivalent to the protractor in the measurement of Cobb angles.

A systematic review of environmental correlates of obesity-related dietary behaviors in youth

There is increasing interest in the role the environment plays in shaping the dietary behavior of youth, particularly in the context of obesity prevention. An overview of environmental factors associated with obesity-related dietary behaviors among youth is needed to inform the development of interventions. A systematic review of observational studies on environmental correlates of energy, fat, fruit/ vegetable, snack/fast food and soft drink intakes in children (4–12 years) and adolescents (13–18 years) was conducted. The results were summarized using the analysis grid for environments linked to obesity. The 58 papers reviewed mostly focused on sociocultural and economical–environmental factors at the household level. The most consistent associations were found between parental intake and children’s fat, fruit/vegetable intakes, parent and sibling intake with adolescent’s energy and fat intakes and parental education with adolescent’s fruit/ vegetable intake. A less consistent but positive association was found for availability and accessibility on children’s fruit/vegetable intake. Environmental factors are predominantly studied at the household level and focus on sociocultural and economic aspects. Most consistent associations were found for parental influences (parental intake and education).More studies examining environmental factors using longitudinal study designs and validated measures are needed for solid evidence to inform interventions.

Protocol engineering for protection against denial-of-service attacks

Denial-of-service attacks (DoS) and distributed denial-of-service attacks (DDoS) attempt to temporarily disrupt users or computer resources to cause service un- availability to legitimate users in the internetworking system. The most common type of DoS attack occurs when adversaries °ood a large amount of bogus data to interfere or disrupt the service on the server. The attack can be either a single-source attack, which originates at only one host, or a multi-source attack, in which multiple hosts coordinate to °ood a large number of packets to the server. Cryptographic mechanisms in authentication schemes are an example ap- proach to help the server to validate malicious tra±c. Since authentication in key establishment protocols requires the veri¯er to spend some resources before successfully detecting the bogus messages, adversaries might be able to exploit this °aw to mount an attack to overwhelm the server resources. The attacker is able to perform this kind of attack because many key establishment protocols incorporate strong authentication at the beginning phase before they can iden- tify the attacks. This is an example of DoS threats in most key establishment protocols because they have been implemented to support con¯dentiality and data integrity, but do not carefully consider other security objectives, such as availability. The main objective of this research is to design denial-of-service resistant mechanisms in key establishment protocols. In particular, we focus on the design of cryptographic protocols related to key establishment protocols that implement client puzzles to protect the server against resource exhaustion attacks. Another objective is to extend formal analysis techniques to include DoS- resistance. Basically, the formal analysis approach is used not only to analyse and verify the security of a cryptographic scheme carefully but also to help in the design stage of new protocols with a high level of security guarantee. In this research, we focus on an analysis technique of Meadows' cost-based framework, and we implement DoS-resistant model using Coloured Petri Nets. Meadows' cost-based framework is directly proposed to assess denial-of-service vulnerabil- ities in the cryptographic protocols using mathematical proof, while Coloured Petri Nets is used to model and verify the communication protocols using inter- active simulations. In addition, Coloured Petri Nets are able to help the protocol designer to clarify and reduce some inconsistency of the protocol speci¯cation. Therefore, the second objective of this research is to explore vulnerabilities in existing DoS-resistant protocols, as well as extend a formal analysis approach to our new framework for improving DoS-resistance and evaluating the performance of the new proposed mechanism. In summary, the speci¯c outcomes of this research include following results; 1. A taxonomy of denial-of-service resistant strategies and techniques used in key establishment protocols; 2. A critical analysis of existing DoS-resistant key exchange and key estab- lishment protocols; 3. An implementation of Meadows's cost-based framework using Coloured Petri Nets for modelling and evaluating DoS-resistant protocols; and 4. A development of new e±cient and practical DoS-resistant mechanisms to improve the resistance to denial-of-service attacks in key establishment protocols.

SELinux policy management framework for HIS

Health Information Systems (HIS) make extensive use of Information and Communication Technologies (ICT). The use of ICT aids in improving the quality and efficiency of healthcare services by making healthcare information available at the point of care (Goldstein, Groen, Ponkshe, and Wine, 2007). The increasing availability of healthcare data presents security and privacy issues which have not yet been fully addressed (Liu, Caelli, May, and Croll, 2008a). Healthcare organisations have to comply with the security and privacy requirements stated in laws, regulations and ethical standards, while managing healthcare information. Protecting the security and privacy of healthcare information is a very complex task (Liu, May, Caelli and Croll, 2008b). In order to simplify the complexity of providing security and privacy in HIS, appropriate information security services and mechanisms have to be implemented. Solutions at the application layer have already been implemented in HIS such as those existing in healthcare web services (Weaver et al., 2003). In addition, Discretionary Access Control (DAC) is the most commonly implemented access control model to restrict access to resources at the OS layer (Liu, Caelli, May, Croll and Henricksen, 2007a). Nevertheless, the combination of application security mechanisms and DAC at the OS layer has been stated to be insufficient in satisfying security requirements in computer systems (Loscocco et al., 1998). This thesis investigates the feasibility of implementing Security Enhanced Linux (SELinux) to enforce a Role-Based Access Control (RBAC) policy to help protect resources at the Operating System (OS) layer. SELinux provides Mandatory Access Control (MAC) mechanisms at the OS layer. These mechanisms can contain the damage from compromised applications and restrict access to resources according to the security policy implemented. The main contribution of this research is to provide a modern framework to implement and manage SELinux in HIS. The proposed framework introduces SELinux Profiles to restrict access permissions over the system resources to authorised users. The feasibility of using SELinux profiles in HIS was demonstrated through the creation of a prototype, which was submitted to various attack scenarios. The prototype was also subjected to testing during emergency scenarios, where changes to the security policies had to be made on the spot. Attack scenarios were based on vulnerabilities common at the application layer. SELinux demonstrated that it could effectively contain attacks at the application layer and provide adequate flexibility during emergency situations. However, even with the use of current tools, the development of SELinux policies can be very complex. Further research has to be made in order to simplify the management of SELinux policies and access permissions. In addition, SELinux related technologies, such as the Policy Management Server by Tresys Technologies, need to be researched in order to provide solutions at different layers of protection.

The effects of habitat fragmentation on the demography and population genetic structure of Uromys Caudimaculatus

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

Effective web service discovery using a combination of a semantic model and a data mining technique

With the advent of Service Oriented Architecture, Web Services have gained tremendous popularity. Due to the availability of a large number of Web services, finding an appropriate Web service according to the requirement of the user is a challenge. This warrants the need to establish an effective and reliable process of Web service discovery. A considerable body of research has emerged to develop methods to improve the accuracy of Web service discovery to match the best service. The process of Web service discovery results in suggesting many individual services that partially fulfil the user’s interest. By considering the semantic relationships of words used in describing the services as well as the use of input and output parameters can lead to accurate Web service discovery. Appropriate linking of individual matched services should fully satisfy the requirements which the user is looking for. This research proposes to integrate a semantic model and a data mining technique to enhance the accuracy of Web service discovery. A novel three-phase Web service discovery methodology has been proposed. The first phase performs match-making to find semantically similar Web services for a user query. In order to perform semantic analysis on the content present in the Web service description language document, the support-based latent semantic kernel is constructed using an innovative concept of binning and merging on the large quantity of text documents covering diverse areas of domain of knowledge. The use of a generic latent semantic kernel constructed with a large number of terms helps to find the hidden meaning of the query terms which otherwise could not be found. Sometimes a single Web service is unable to fully satisfy the requirement of the user. In such cases, a composition of multiple inter-related Web services is presented to the user. The task of checking the possibility of linking multiple Web services is done in the second phase. Once the feasibility of linking Web services is checked, the objective is to provide the user with the best composition of Web services. In the link analysis phase, the Web services are modelled as nodes of a graph and an allpair shortest-path algorithm is applied to find the optimum path at the minimum cost for traversal. The third phase which is the system integration, integrates the results from the preceding two phases by using an original fusion algorithm in the fusion engine. Finally, the recommendation engine which is an integral part of the system integration phase makes the final recommendations including individual and composite Web services to the user. In order to evaluate the performance of the proposed method, extensive experimentation has been performed. Results of the proposed support-based semantic kernel method of Web service discovery are compared with the results of the standard keyword-based information-retrieval method and a clustering-based machine-learning method of Web service discovery. The proposed method outperforms both information-retrieval and machine-learning based methods. Experimental results and statistical analysis also show that the best Web services compositions are obtained by considering 10 to 15 Web services that are found in phase-I for linking. Empirical results also ascertain that the fusion engine boosts the accuracy of Web service discovery by combining the inputs from both the semantic analysis (phase-I) and the link analysis (phase-II) in a systematic fashion. Overall, the accuracy of Web service discovery with the proposed method shows a significant improvement over traditional discovery methods.