Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology

Discovery of cis-regulatory elements in gene promoters is a highly challenging research issue in computational molecular biology. This paper presents a novel approach to searching putative cis-regulatory elements in human promoters by first finding 8-mer sequences of high statistical significance from gene promoters of humans, mice, and Drosophila melanogaster, respectively, and then identifying the most conserved ones across the three species (phylogenetic footprinting). In this study, a conservation analysis on both closely related species (humans and mice) and distantly related species (humans/mice and Drosophila) is conducted not only to examine more candidates but also to improve the prediction accuracy. We have found 124 putative cis-regulatory elements and grouped these into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters reveals that SP1, EGR, and NRF-1 are the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene Ontology (GO) analysis also shows that many GO categories of transcription factors binding to these cis-regulatory elements match the GO categories of genes whose promoters contain these elements. Compared with previous research, the contribution of this study lies not only in the finding of new cis-regulatory elements, but also in its pioneering exploration on the coexistence of discovered elements and the GO relationship between transcription factors and regulated genes. This exploration verifies the putative cis-regulatory elements that have been found from this study and also gives new insight on the regulation mechanisms of gene expression.

Opportunity and risk management for complex oil and gas developments

The thesis examines complex new oil and gas field developments, when growing the business from current capabilities and practice to the frontiers of undeveloped reservoirs. The contributors to complexity were identified, and an integrated methodology for opportunity and risk management, assessment and analysis was developed to produce more credible forecasts.

Safeguard information infrastructure against DDoS attacks: experiments and modeling

Nowadays Distributed Denial of Service (DDoS) attacks have made one of the most serious threats to the information infrastructure. In this paper we firstly present a new filtering approach, Mark-Aided Distributed Filtering (MADF), which is to find the network anomalies by using a back-propagation neural network, deploy the defense system at distributed routers, identify and filtering the attack packets before they can reach the victim; and secondly propose an analytical model for the interactions between DDoS attack party and defense party, which allows us to have a deep insight of the interactions between the attack and defense parties. According to the experimental results, we find that MADF can detect and filter DDoS attack packets with high sensitivity and accuracy, thus provide high legitimate traffic throughput and low attack traffic throughput. Through the comparison between experiments and numerical results, we also demonstrate the validity of the analytical model that can precisely estimate the effectiveness of a DDoS defense system before it encounters different attacks.

Teachers' perceptions of their abilities to be educational leaders in Victorian childcare settings

In the context of new national regulatory requirements for designated educational leaders in early childhood settings, 11 Victorian teachers participated in semi-structured interviews exploring their perceptions of their ability to act as educational leaders in their childcare centres. Analysis of these interviews showed that, while teachers successfully made changes within their rooms, only those with a formal title or authority expressed confidence in their ability to lead change across their centres. Barriers to leadership included lack of time and a perception that their teacher qualifications 'did not buy authority'. A hierarchical model of leadership appeared dominant within the centres. The findings suggest both time allowance and formal role designation as strategies to support the new leadership roles, but also raise questions about the most effective models for supporting teacher leadership in childcare contexts.

Regulatory and enabling approaches to corporate law enforcement : patterns of litigation 1986-2002 and the effect of recent reforms in New Zealand, Australia and the United Kingdom

Enforcement of corporate rights and duties may follow either a ‘regulatory’ or ‘enabling’ model. If a regulatory approach is taken, enforcement action will generally be undertaken by regulatory agencies such as, in New Zealand, the Registrar of Companies and Securities Commission, the Australian Securities and Investments Commission (ASIC) or the Department of Trade and Industry (DTI) in the United Kingdom. If an enabling approach is chosen, enforcement action will more often be by private parties such as company shareholders, directors or creditors. When New Zealand's company law was reformed in 1993, a primarily private enforcement regime was adopted, consisting of a list of statutory directors' duties and an enhanced collection of shareholder remedies, based in part upon North American models and including a statutory derivative action. Public enforcement was largely confined to administrative matters and the enforcement of the disclosure requirements of New Zealand's securities law. While the previous enforcement regime was similarly reliant on private action, the law on directors' duties was less accessible, and shareholder action was hindered by the majority rule principle and the rule in Foss v Harbottle. This approach is in contrast with that used in Australia and the United Kingdom, where public agencies have a much more prominent enforcement role despite recent and proposed reforms to directors' duties and shareholder remedies. These reforms are designed to improve the ability of private parties to enforce corporate rights and duties. A survey of enforcement litigation in New Zealand since 1986 indicates that the object of a primarily enabling enforcement regime seems to have been achieved, and may well have been achieved even without the 1993 reform package. Private enforcement has, in fact, been much more prevalent than public enforcement since well before the enactment of the new legislation. Most enforcement action both before and after the reform was commenced by shareholders and shareholder/directors, and most involved closely held companies. Public enforcement was largely undertaken in areas such as securities law, where the wider public interest was affected. Similar surveys of Australian and United Kingdom enforcement litigation reveal a proportionally much greater reliance on public bodies to enforce corporate rights and duties, indicating a more regulatory approach. The ASIC and DTI enforced a wider range of provisions, affecting both closely and widely held companies, than those subject to public enforcement in New Zealand. Publicly enforced provisions in Australia and the United Kingdom include directors' duties and provisions dealing with disqualification from managing companies, as well as securities law requirements.

A new method to warm up lubricating oil to improve the fuel efficiency during cold start

Cold start driving cycles exhibit an increase in friction losses due to the low temperatures of metal and media compared to normal operating engine conditions. These friction losses are responsible for up to 10% penalty in fuel economy over the official drive cycles like the New European Drive Cycle (NEDC), where the temperature of the oil even at the end of the 1180 s of the drive cycle is below the fully warmed up values of between 100°C and 120°C. At engine oil temperatures below 100°C the water from the blow by condensates and dilutes the engine oil in the oil pan which negatively affects engine wear. Therefore engine oil temperatures above 100°C are desirable to minimize engine wear through blow by condensate. The paper presents a new technique to warm up the engine oil that significantly reduces the friction losses and therefore also reduces the fuel economy penalty during a 22°C cold start NEDC. Chassis dynamometer experiments demonstrated fuel economy improvements of over 7% as well as significant emission reductions by rapidly increasing the oil temperature. Oil temperatures were increased by up to 60°C during certain parts of the NEDC. It is shown how a very simple sensitivity analysis can be used to assess the relative size or efficiency of different heat transfer passes and the resulting fuel economy improvement potential of different heat recovery systems system. Due to its simplicity the method is very fast to use and therefore also very cost effective. The method demonstrated a very good correlation for the fuel consumption within ±1% compared to measurements on a vehicle chassis roll.

New crevice corrosion testing method and its use in the investigation of oil stain

A new electrochemical method was developed to investigate crevice corrosion and its inhibitors. A wire beam electrode was used to allow electrochemical parameters to be measured directly from the crevice area. As an example, oil stain was investigated using this method.

Do oil prices predict economic growth? New global evidence

In this paper, we test whether oil price predicts economic growth for 28 developed and 17 developing countries. We use predictability tests that account for the key features of the data, namely, persistency, endogeneity, and heteroskedasticity. Our analysis considers a large number of countries, shows evidence of more out-of-sample predictability with nominal than real oil prices, finds in-sample predictability to be independent of the use of nominal and real prices, and reveals greater evidence of predictability for developed countries.

Lipase-catalysed incorporation of EPA into emu oil: formation and characterisation of new structured lipids

Partial hydrolysis of emu oil was performed using Thermomyces lanuginosus lipase to remove some shorter chain fatty acids. Then eicosapentaenoic acid (EPA) was incorporated into the modified emu oil using either Lipozyme RMIM or Lipozyme TLIM to produce new EPA enriched structured lipids. Using Isooctane as a reaction solvent increased the level of EPA incorporation, which was higher with RMIM than with TLIM. TLIM incorporated EPA almost exclusively into the sn-1,3 positions, whereas RMIM incorporated EPA at sn-1,3 and sn-2 positions in an almost statistical ratio. Both structured lipids were less oxidatively stable than emu oil.

The isolation and identification of new microalgal strains producing oil and carotenoid simultaneously with biofuel potential

Taxonomy and phylogeny of twenty two microalgal isolates were examined using both universal and newly designed molecular primers. Among the isolates, Scenedesmus bijugus, Coelastrella sp., Auxenochlorella protothecoides, and Chlorella sp. were particularly promising in terms of producing lipids as measured by fatty acid methyl esters (FAME) analysis and significant concentration of carotenoids. A comparative experiment showed that S. bijugus and Chlorella sp. were the most promising candidates (L(-)(1)d(-)(1), with biomass) 174.77±6.75, 169.81±5.22mg, lipids 40.14±3.31, 39.72±3.89mg, lutein 0.47, 0.36mg, and astaxanthin 0.27, 0.18mg respectively. The fatty acids produced by these microalgal isolates were mainly palmitic, stearic, oleic, linoleic, and linolenic acid. The freshwater microalgal isolate S. bijugus be the most suitable isolate for producing biodiesel and carotenoids, due to high productivity of biomass, lipids, metabolites, and its suitable fatty acid profile.

New voice, same story? Social entrepreneurship and active social capital formation

The development of the third sector in Australia has involved the negotiation of varying forms of state and market regulatory mechanisms. In the course of these settlements, ground-up initiatives have often found that authenticity is only the starting point on journeys that end in incorporation. Social entrepreneurship is an emerging set of ideas which attempts to hold on to the authentic and unique elements generated by grassroots actions. What are its chances of success? This article sets out to answer this question through a discussion of regulation and social capital. A four-fold model of social cap ita I formation is advanced which outlines 'defensive', 'consolidative', 'inclusive' and 'regulated' social capital. It is concluded that while social entrepreneurship has the potential to shift social capital formation from reactive to active forms, it is likely to become increasingly standardised and regulated.

Observations on ponticocythereis tricristata (Brady, 1880) from the Admiralty Islands, Papua New Guinea and comments on quaternary ostracod evolution within the sw Pacific Ocean

The ostracod species originally described as Cythere tricristata Brady, 1880 from the Admiralty Islands, Papua New Guinea, appears to belong to the SW Pacific and Australasian genus Ponticocythereis McKenzie, 1967 (sensu Warne & Whatley 1996). This interpretation is based on the presence of some posterior pointing scale-like spines on the carapace surface of this species. SEM images of the type material for Ponticocythereis tricristara n. comb., which are presented here for the first time, enable the clear differentiation of this species from the very similar Ponticocythereis ichthyoderma (Brady, 1890), Ponticocythereis quadriserialis (Brady, 1890) and Ponticocythereis laingensis (Wouters, 1981). As a consequence of the subdued manifestation of scale-like or blade-like spines on adult specimens of P. tricristata, this species closely resembles juvenile rather than adult specimens of some other Ponticocythereis species. This ontogenetic/phylogenetic relationship suggests that paedomorphic processes were significant in the Quaternary evolutionary radiation of Ponticocythereis species within tropical SW Pacific and Australasian regions.

A custom-built insulin resistance gene chip

Objectives/Aim—Microarray (gene chip) technology offers a powerful new tool for analyzing the expression of large numbers of genes in many experimental samples. The aim of this study was to design, construct, and use a gene chip to measure the expression levels of key genes in metabolic pathways related to insulin resistance.
Methods—We selected genes that were implicated in the development of insulin resistance, including genes involved in insulin signaling; glucose uptake, oxidation, and storage; fat uptake, oxidation, and storage; cytoskeletal components; and transcription factors. The key regulatory genes in the pathways were identified, along with other recently identified candidate genes such as calpain-10. A total of 242 selected genes (including 32 internal control elements) were sequence-verified, purified, and arrayed on aldehyde-coated slides.
Results—Where more than 1 clone containing the gene of interest was available, we chose those containing the genes in the 5' orientation and an insert size of around 1.5 kb. Of the 262 clones purchased, 56 (21%) were found to contain sequences other than those expected. In addition, 2 (1%) did not grow under standard conditions and were assumed to be nonviable. In these cases, alternate clones containing the gene of interest were chosen as described above. The current version of the Insulin Resistance Gene Chip contains 210 genes of interest, plus 48 control elements. A full list of the genes is available at http://www.hbs.deakin.edu.au/mru/research/gene_chip_tech/genechip_three.htm/.
Conclusions—The human Insulin Resistance Gene Chip that we have constructed will be a very useful tool for investigating variation in the expression of genes relevant to insulin resistance under various experimental conditions. Initially, the gene chip will be used in studies such as exercise interventions, fasting, euglycemic-hyperinsulinemic clamps, and administration of antidiabetic agents

Observations of loxocythere (loxocythere) ouyenensis (chapman, 1914) (ostracoda) from the cenozoic of S.E. Australia with comments on species attributed to microcytherura müller, 1894 and hemiparvocythere hartmann, 1982 from Australian and New Zealand ma

The type material of Loxocythere (Loxocythere) ouyenensis (Chapman, 1914) from mid Cenozoic strata of the Mallee Bore No. 11 in the Murray Basin, S.E. Australia is partially redescribed and refigured. This species belongs to a discrete group of large elongate Cenozoic fossil and living Loxocythere species, the carapaces of which possess sub-rectangular inner margin outlines, and broadly rounded posterior extremities. Some much smaller but otherwise very similarly shaped species, that have previously been placed under the genus Microcytherura (i.e. Microcytherura? peterroyi Yassini and Jones, 1995) or the genus Hemiparvocythere Hartmann, 1982 (i.e. Hemiparvocythere Iagunicola Hartmann, 1982), are also known from marine Cenozoic strata and modern seas of the Australasian region. There is a marked difference in the shape of the inner margin between this group of small Australasian forms and European species of Microcytherura s.s .. The former have broadly rounded posterior inner margins, whilst the latter have acutely rounded posterior inner margins. The latter also usually present posterior extremities located well below mid carapace height. It is here argued that this difference in inner margin shape between smaller Australasian species such as Microcytherura? peterroyi, and European species of Microcytherura s.s ., suggests that there is not a direct phylogenetic relationship between these two species groups.