The Gerbera cDNA Microarray: A Tool for Large-Scale Identification of Genes Involved in Flower Development

During the past ten years, large-scale transcript analysis using microarrays has become a powerful tool to identify and predict functions for new genes. It allows simultaneous monitoring of the expression of thousands of genes and has become a routinely used tool in laboratories worldwide. Microarray analysis will, together with other functional genomics tools, take us closer to understanding the functions of all genes in genomes of living organisms. Flower development is a genetically regulated process which has mostly been studied in the traditional model species Arabidopsis thaliana, Antirrhinum majus and Petunia hybrida. The molecular mechanisms behind flower development in them are partly applicable in other plant systems. However, not all biological phenomena can be approached with just a few model systems. In order to understand and apply the knowledge to ecologically and economically important plants, other species also need to be studied. Sequencing of 17 000 ESTs from nine different cDNA libraries of the ornamental plant Gerbera hybrida made it possible to construct a cDNA microarray with 9000 probes. The probes of the microarray represent all different ESTs in the database. From the gerbera ESTs 20% were unique to gerbera while 373 were specific to the Asteraceae family of flowering plants. Gerbera has composite inflorescences with three different types of flowers that vary from each other morphologically. The marginal ray flowers are large, often pigmented and female, while the central disc flowers are smaller and more radially symmetrical perfect flowers. Intermediate trans flowers are similar to ray flowers but smaller in size. This feature together with the molecular tools applied to gerbera, make gerbera a unique system in comparison to the common model plants with only a single kind of flowers in their inflorescence. In the first part of this thesis, conditions for gerbera microarray analysis were optimised including experimental design, sample preparation and hybridization, as well as data analysis and verification. Moreover, in the first study, the flower and flower organ-specific genes were identified. After the reliability and reproducibility of the method were confirmed, the microarrays were utilized to investigate transcriptional differences between ray and disc flowers. This study revealed novel information about the morphological development as well as the transcriptional regulation of early stages of development in various flower types of gerbera. The most interesting finding was differential expression of MADS-box genes, suggesting the existence of flower type-specific regulatory complexes in the specification of different types of flowers. The gerbera microarray was further used to profile changes in expression during petal development. Gerbera ray flower petals are large, which makes them an ideal model to study organogenesis. Six different stages were compared and specifically analysed. Expression profiles of genes related to cell structure and growth implied that during stage two, cells divide, a process which is marked by expression of histones, cyclins and tubulins. Stage 4 was found to be a transition stage between cell division and expansion and by stage 6 cells had stopped division and instead underwent expansion. Interestingly, at the last analysed stage, stage 9, when cells did not grow any more, the highest number of upregulated genes was detected. The gerbera microarray is a fully-functioning tool for large-scale studies of flower development and correlation with real-time RT-PCR results show that it is also highly sensitive and reliable. Gene expression data presented here will be a source for gene expression mining or marker gene discovery in the future studies that will be performed in the Gerbera Laboratory. The publicly available data will also serve the plant research community world-wide.

An open source service oriented Mobile Business Intelligence Tool (MBIT)

Corporate executives require relevant and intelligent business information in real-time to take strategic decisions. They require the freedom to access this information anywhere and anytime. There is a need to extend this functionality beyond the office and on the fingertips of the decision makers. Mobile Business Intelligence Tool (MBIT) aims to provide these features in a flexible and cost-efficient manner. This paper describes the detailed architecture of MBIT to overcome the limitations of existing mobile business intelligence tools. Further, a detailed implementation framework is presented to realize the design. This research highlights the benefits of using service oriented architecture to design flexible and platform independent mobile business applications. © 2009 IEEE.

Mathematical model and rule extraction for tool wear monitoring problem using nature inspired techniques

In this paper, pattern classification problem in tool wear monitoring is solved using nature inspired techniques such as Genetic Programming(GP) and Ant-Miner (AM). The main advantage of GP and AM is their ability to learn the underlying data relationships and express them in the form of mathematical equation or simple rules. The extraction of knowledge from the training data set using GP and AM are in the form of Genetic Programming Classifier Expression (GPCE) and rules respectively. The GPCE and AM extracted rules are then applied to set of data in the testing/validation set to obtain the classification accuracy. A major attraction in GP evolved GPCE and AM based classification is the possibility of obtaining an expert system like rules that can be directly applied subsequently by the user in his/her application. The performance of the data classification using GP and AM is as good as the classification accuracy obtained in the earlier study.

The research capacity and culture of Australian podiatrists

Background Best practice clinical health care is widely recognised to be founded on evidence based practice. Enhancing evidence based practice via the rapid translation of new evidence into every day clinical practice is fundamental to the success of health care and in turn health care professions. There is little known about the collective research capacity and culture of the podiatry profession across Australia. Thus, the aim of this study was to investigate the research capacity and culture of the podiatry profession within Australia and determine if there were any differences between podiatrists working in different health sectors and workplaces. Method All registered podiatrists were eligible to participate in a cross-sectional online survey. The Australian Podiatry Associations disseminated the survey and all podiatrists were encouraged to distribute it to colleagues. The Research Capacity and Culture (RCC) tool was used to collect all research capacity and culture item variables using a 10-point scale (1 = lowest; 10 = highest). Additional demographic, workplace and health sector data variables were also collected. Mann–Whitney-U, Kruskal–Wallis and logistic regression analyses were used to determine any difference between health sectors and workplaces. Word cloud analysis was used for qualitative responses of individual motivators and barriers to research culture. Results There were 232 fully completed surveys (6% of Australian registered podiatrists). Overall respondents reported low success or skills (Median rating < 4) on the majority of individual success or skill items. Podiatrists working in multi-practitioner workplaces reported higher individual success or skills in the majority of items compared with sole practitioners (p < 0.05). Non-clinical and public health sector podiatrists reported significantly higher post-graduate study enrolment or completion, research activity participation, provisions to undertake research and individual success or skill than those working privately. Conclusions This study suggests that podiatrists in Australia report similar low levels of research success or skill to those reported in other allied health professions. The workplace setting and health sector seem to play key roles in self reported research success and skills. This is important knowledge for podiatrists and researchers aiming to translate research evidence into clinical practice.

A flexible tool for integrated planning of active distribution networks

This paper presents a flexible and integrated planning tool for active distribution network to maximise the benefits of having high level s of renewables, customer engagement, and new technology implementations. The tool has two main processing parts: “optimisation” and “forecast”. The “optimization” part is an automated and integrated planning framework to optimize the net present value (NPV) of investment strategy for electric distribution network augmentation over large areas and long planning horizons (e.g. 5 to 20 years) based on a modified particle swarm optimization (MPSO). The “forecast” is a flexible agent-based framework to produce load duration curves (LDCs) of load forecasts for different levels of customer engagement, energy storage controls, and electric vehicles (EVs). In addition, “forecast” connects the existing databases of utility to the proposed tool as well as outputs the load profiles and network plan in Google Earth. This integrated tool enables different divisions within a utility to analyze their programs and options in a single platform using comprehensive information.

EIT as a tool to observe dual wavelength operation of a semiconductor laser

We propose a simplified technique for dual wavelength operation of an extended cavity semiconductor laser, and its characterization using electromagnetically induced transparency (EIT). In this laser cavity scheme light beam is made converging before it incidences on the cavity grating. The converging angle of the beam creates two longitudinal oscillating modes of resonating cavity. Frequency separation between the longitudinal modes are measured with the help of beat frequency generation in a photodiode and creating pair of EIT spectra in Rb vapor. The pair of EIT dips that are generated due to dual wavelength of this laser (that is used as control laser) can be used to estimate frequency difference between the generated wavelengths. Width of EIT spectra can be used to estimate line width of individual wavelength components.

Fluorescence polarization as a tool to study lectin-sugar interaction. An investigation of the binding of 4-methylumbelliferyl beta-D-galactopyranoside to Abrus precatorious agglutinin

Polarization of ligand fluorescence was used to study the binding of 4-methylumbelliferyl beta-D-galactopyranoside (MeUmb-Galp) to Abrus precatorious agglutinin. The binding of the fluorescent sugar to the lectin led to considerable polarization of the MeUmb-Galp fluorescence, which was also quenched by about 30% on binding to the lectin. The binding of the fluorescent sugar was carbohydrate-specific, as evidenced by inhibition of both fluorescence polarization and quenching when lectin was preincubated with lactose. The association constant as determined by fluorescence polarization is 1.42 x 10(4) M-1 at 25 degrees C and is in excellent agreement with those determined by fluorescence quenching (Ka = 1.51 x 10(4) M-1) and equilibrium dialysis (Ka = 1.62 x 10(4) M-1) at 25 degrees C. The numbers of binding sites as determined by fluorescence polarization, quenching and equilibrium dialysis agree very well with one another, n being equal to 2.0 +/- 0.05. The consistency between the association constant value determined by fluorescence polarization, quenching and equilibrium dialysis shows the validity of this approach to study lectin-sugar interaction.

Influence of tool rake angle on the quality of pure magnesium chip-consolidated product

Chips were produced by orthogonal Cutting of cast pure magnesium billet with three different tool rake angles viz., -15 degrees, -5 degrees and +15 degrees on a lathe. Chip consolidation by solid state recycling technique involved cold compaction followed by hot extrusion. The extruded products were characterized for microstructure and mechanical properties. Chip-consolidated products from -15 degrees rake angle tools showed 19% increase in tensile strength, 60% reduction ingrain size and 12% increase in hardness compared to +15 degrees rake chip-consolidated product indicating better chip bonding and grain refinement. Microstructure of the fracture specimen Supports the abovefinding. On the overall, the present work high lights the importance of tool take angle in determining the quality of the chip-consolidated products. (C) 2009 Elsevier B.V. All rights reserved.

A Single Mammalian Mitochondrial Translation Initiation Factor Functionally Replaces Two Bacterial Factors

The mechanism of translation in eubacteria and organelles is thought to be similar. In eubacteria, the three initiation factors IF1, IF2, and IF3 are vital. Although the homologs of IF2 and IF3 are found in mammalian mitochondria, an IF1 homolog has never been detected. Here, we show that bovine mitochondrial IF2 (IF2mt) complements E. coli containing a deletion of the IF2 gene (E. coli ΔinfB). We find that IF1 is no longer essential in an IF2mt-supported E. coli ΔinfB strain. Furthermore, biochemical and molecular modeling data show that a conserved insertion of 37 amino acids in the IF2mt substitutes for the function of IF1. Deletion of this insertion from IF2mt supports E. coli for the essential function of IF2. However, in this background, IF1 remains essential. These observations provide strong evidence that a single factor (IF2mt) in mammalian mitochondria performs the functions of two eubacterial factors, IF1 and IF2.

Prostate cancer organoids: A potential new tool for testing drug sensitivity

Recent technical advances have enabled for the first time, reliable in vitro culture of prostate cancer samples as prostate cancer organoids. This breakthrough provides the significant possibility of high throughput drug screening covering the spectrum of prostate cancer phenotypes seen clinically. These advances will enable precision medicine to become a reality, allowing patient samples to be screened for effective therapeutics ex vivo, with tailoring of treatments specific to that individual. This will hopefully lead to enhanced clinical outcomes, avoid morbidity due to ineffective therapies and improve the quality of life in men with advanced prostate cancer.

Sentinel lymph node biopsy as a diagnostic tool in the treatment of breast cancer

The purpose of this study was to evaluate the use of sentinel node biopsy (SNB) in the axillary nodal staging in breast cancer. A special interest was in sentinel node (SN) visualization, intraoperative detection of SN metastases, the feasibility of SNB in patients with pure tubular carcinoma (PTC) and in those with ductal carcinoma in situ (DCIS) in core needle biopsy (CNB) and additionally in the detection of axillary recurrences after tumour negative SNB. Patients and methods. 1580 clinically stage T1-T2 node-negative breast cancer patients, who underwent lymphoscintigraphy (LS), SNB and breast surgery between June 2000 - 2004 at the Breast Surgery Unit. The CNB samples were obtained from women, who participated the biennial, population based mammography screening at the Mammography Screening Centre of Helsinki 2001 - 2004.In the follow- up, a cohort of 205 patients who avoided AC due to negative SNB findings were evaluated using ultrasonography one and three years after breast surgery. Results. The visualization rate of axillary SNs was not enhanced by adjusting radioisotope doses according to BMI. The sensitivity of the intraoperative diagnosis of SN metastases of invasive lobular carcinoma (ILC) was higher, 87%, with rapid, intraoperative immunohistochemistry (IHC) group compared to 66% without it. The prevalence of tumour positive SN findings was 27% in the 33 patients with breast tumours diagnosed as PTC. The median histological tumour size was similar in patients with or without axillary metastases. After the histopathological review, six out of 27 patients with true PTC had axillary metastases, with no significant change in the risk factors for axillary metastases. Of the 67 patients with DCIS in the preoperative percutaneous biopsy specimen , 30% had invasion in the surgical specimen. The strongest predictive factor for invasion was the visibility of the lesion in ultrasound. In the three year follow-up, axillary recurrence was found in only two (0.5%) of the total of 383 ultrasound examinations performed during the study, and only one of the 369 examinations revealed cancer. None of the ultrasound examinations were false positive, and no study participant was subjected to unnecessary surgery due to ultrasound monitoring. Conclusions. Adjusting the dose of the radioactive tracer according to patient BMI does not increase the visualization rate of SNs. The intraoperative diagnosis of SN metastases is enhanced by rapid IHC particularly in patients with ILC. SNB seems to be a feasible method for axillary staging of pure tubular carcinoma in patients with a low prevalence of axillary metatastases. SNB also appears to be a sensible method in patients undergoing mastectomy due to DCIS in CNB. It also seems useful in patients with lesions visible in breast US. During follow-up, routine monitoring of the ipsilateral axilla using US is not worthwhile among breast cancer patients who avoided AC due to negative SN findings.

A journey access tool to facilitate mobility-related access for people with disabilities in low and middle income countries

People with disabilities (PWD) experience difficulties in accessing the transport system (including both infrastructure and services) to meet their needs for health care, employment and other activities. Our research shows that lack of access to the journeys needed for these purposes is a more significant barrier in low and middle income countries than in high income countries, and results in inadequate health care, rehabilitation and access to education and employment. At the same time, the existing transport system in low and middle income countries presents much higher road crash risks than in high income countries. By combining the principles and methods of Road Safety Audit and disability access, and adapting these Western approaches to a low/middle income country context, we have worked with Handicap International Cambodia to develop a Journey Access Tool (JAT) for use by disabled peoples’ organisations (DPOs), people with a disability and other key stakeholders. A key element of the approach is that it involves the participation of PWD on the journeys that they need to take, and it identifies infrastructure and service improvements that should be prioritised in order to facilitate access to these journeys. The JAT has been piloted in Cambodia with a range of PWD. This presentation will outline the design of the JAT and the results of the pilot studies. The information gained thus far strongly suggests that the JAT is a valuable and cost-effective approach that can be used by DPOs and professionals to identify barriers to access and prioritise the steps needed to address them.

COMPASS – A tool for evaluation of compression strategies for embedded processors

A major concern of embedded system architects is the design for low power. We address one aspect of the problem in this paper, namely the effect of executable code compression. There are two benefits of code compression – firstly, a reduction in the memory footprint of embedded software, and secondly, potential reduction in memory bus traffic and power consumption. Since decompression has to be performed at run time it is achieved by hardware. We describe a tool called COMPASS which can evaluate a range of strategies for any given set of benchmarks and display compression ratios. Also, given an execution trace, it can compute the effect on bus toggles, and cache misses for a range of compression strategies. The tool is interactive and allows the user to vary a set of parameters, and observe their effect on performance. We describe an implementation of the tool and demonstrate its effectiveness. To the best of our knowledge this is the first tool proposed for such a purpose.