Quantitative stem-loop RT-PCR for detection of microRNAs

Plant microRNAs (miRNAs) are a class of endogenous small RNAs that are essential for plant development and survival. They arise from larger precursor RNAs with a characteristic hairpin structure and regulate gene activity by targeting mRNA transcripts for cleavage or translational repression. Efficient and reliable detection and quantification of miRNA expression has become an essential step in understanding their specific roles. The expression levels of miRNAs can vary dramatically between samples and they often escape detection by conventional technologies such as cloning, northern hybridization and microarray analysis. The stem-loop RT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate and reliable manner. First, a miRNA-specific stem-loop RT primer is hybridized to the miRNA and then reverse transcribed. Next, the RT product is amplified and monitored in real time using a miRNA-specific forward primer and the universal reverse primer. This method enables miRNA expression profiling from as little as 10 pg of total RNA and is suitable for high-throughput miRNA expression analysis.

Chocolate, Jazz and Christmas festivals in Tubingen & Stuttgart

A travel article about southern German festivals. IT WAS Golden October, when a last wave of Italian warmth made it across the Alps into southern Germany. Outside, the final sunlight of the day found the tops of trees, and the town seemed cast entirely in autumn patterns. I followed the busy pedestrian traffic across the Neckar River into the old part of Tübingen.

Mesenchymal-to-epithelial transition facilitates bladder cancer metastasis : role of fibroblast growth factor receptor-2

Epithelial-to-mesenchymal transition (EMT) increases cell migration and invasion, and facilitates metastasis in multiple carcinoma types, but belies epithelial similarities between primary and secondary tumors. This study addresses the importance of mesenchymal-to-epithelial transition (MET) in the formation of clinically significant metastasis. The previously described bladder carcinoma TSU-Pr1 (T24) progression series of cell lines selected in vivo for increasing metastatic ability following systemic seeding was used in this study. It was found that the more metastatic sublines had acquired epithelial characteristics. Epithelial and mesenchymal phenotypes were confirmed in the TSU-Pr1 series by cytoskeletal and morphologic analysis, and by performance in a panel of in vitro assays. Metastatic ability was examined following inoculation at various sites. Epithelial characteristics associated with dramatically increased bone and soft tissue colonization after intracardiac or intratibial injection. In contrast, the more epithelial sublines showed decreased lung metastases following orthotopic inoculation, supporting the concept that EMT is important for the escape of tumor cells from the primary tumor. We confirmed the overexpression of the IIIc subtype of multiple fibroblast growth factor receptors (FGFR) through the TSU-Pr1 series, and targeted abrogation of FGFR2IIIc reversed the MET and associated functionality in this system and increased survival following in vivo inoculation in severe combined immunodeficient mice. This model is the first to specifically model steps of the latter part of the metastatic cascade in isogenic cell lines, and confirms the suspected role of MET in secondary tumor growth.

Carcinoma invasion and metastasis : a role for epithelial-mesenchymal transition?

Carcinogenesis involves the accretion of unprogrammed genetic and epigenetic changes, which lead to dysregulation of the normal control of cell number. But a key clinical turning point in carcinoma progression is the establishment by emigrant cells of secondary growth sites (i.e., metastasis). The metastatic “cascade” comprises numerous steps, including escape from the primary tumor site, penetration of local stroma, entry of local vascular or lymphatic vessels (intravasation), aggregation with platelets, interaction with and adhesion to distant endothelia, extravasation, recolonization, and expansion ( 1), all the time avoiding effective immune clearance and being able to survive in these multiple contexts...

Bluetooth vehicle trajectory by fusing Bluetooth and loops : motorway travel time statistics

Loop detectors are widely used on the motorway networks where they provide point speed and traffic volumes. Models have been proposed for temporal and spatial generalization of speed for average travel time estimation. Advancement in technology provides complementary data sources such as Bluetooth MAC Scanner (BMS), detecting the MAC ID of the Bluetooth devices transported by the traveller. Matching the data from two BMS stations provides individual vehicle travel time. Generally, on the motorways loops are closely spaced, whereas BMS are placed few kilometres apart. In this research, we fuse BMSs and loops data to define the trajectories of the Bluetooth vehicles. The trajectories are utilised to estimate the travel time statistics between any two points along the motorway. The proposed model is tested using simulation and validated with real data from Pacific motorway, Brisbane. Comparing the model with the linear interpolation based trajectory provides significant improvements.

STEM education for sustainable development : a sociotechnical analysis

It is debated that for sustainable STEM education and knowledge investment, human centered learning design approach is critical and important. Sustainability in this context is enduring maintenance of technological trajectories for productive economical and social interactions by demonstrating life critical scenarios through life critical system development and life experiences. Technology influences way of life and the learning and teaching process. Social software application development is more than learning of how to program a software application and extracting information from the Internet. Hence, our research challenge is, how do we attract learners to STEM social software application development? Our realisation processes begin with comparing Science and Technology education in developed (e.g., Australia) and developing (e.g., Sri Lanka) countries with distinction on final year undergraduates’ industry ready training programmes. Principal components analysis was performed to separate patterns of important factors. To measure behavioural intention of perceived usefulness and attitudes of the training, the measurement model was analysed to test its validity and reliability using partial least square (PLS) analysis of structural equation modelling (SEM). Our observation is that the relationship is more complex than we argue for. Our initial conclusions were that life critical system development and life experience trajectories as determinant factors while technological influences were unavoidable. A further investigation should involve correlations between human centered learning design approach and economical development in the long run.

Does usability engineering matters for STEM education?

Technological maturity and the exponential growth of digital applications are contributing to lifestyle changes worldwide. Consequently, learning and teaching is demanding more effective sociotechnical interactions involving emerging technologies, as opposed to traditional, conventional face-to-face learning and teaching approaches. In this context, usability engineering is making significant contributions for improving computer and distance-based learning, both for learners and instructors, which have often been ignored when designing online learning and teaching applications. Usability testing is a central part of the human centered learning approach for developing sustainable STEM education from the socio-technological perspective. Our experiences with usability engineering and the impact of teaching low-cost rapid usability testing methods on knowledge translation from undergraduate to graduate courses to real-world practice (i.e. getting the methods out there in real use) are diverse and multi-modal. Our sample space has been hundreds of trained students who have learned how to do effective usability engineering in real-world situations at higher levels of realism (i.e. fidelity) and at a much lower cost than using traditional fixed usability labs. Furthermore, this low-cost rapid approach to usability engineering has been adopted by many of our graduates who are now managers, CIOs etc and who are using the methods routinely in their organizations in real world applications and scenarios. This knowledge has been used to improve design and implementation of a wide range of applications, including applications designed for teaching and learning.

Mechanisms of tumour invasion and metastasis : emerging targets for therapy

The progression of a tumour from one of benign and delimited growth to one that is invasive and metastatic is the major cause of poor clinical outcome in cancer patients. The invasion and metastasis of tumours is a highly complex and multistep process that requires a tumour cell to modulate its ability to adhere, degrade the surrounding extracellular matrix, migrate, proliferate at a secondary site and stimulate angiogenesis. Knowledge of the process has greatly increased and this has resulted in the identification of a number of molecules that are fundamental to the process. The involvement of these molecules has been shown to relate not only to the survival and proliferation of the tumour cell but, also to the processes of tumour cell adhesion, migration, and the tumour cells ability to degrade and escape the primary site as well as play a role in angiogenesis. These molecules may provide important therapeutic targets that represent the ability to target specific steps in the process of invasion and metastasis and provide additional therapies. The review focuses on representative key targets in each of these processes and summarises the state of play in each case.

Surface insulation performance of epoxy resin/silica nanocomposite material

Composite polymer insulators provide many advantages over the traditional porcelain insulators and they are increasingly being used at both transmission and distribution levels. In the present paper, an epoxy resin/silica nanocomposite dielectric material (NDM) structure is proposed and fabricated. Hydrophobic fumed silica is incorporated in epoxy resin matrix and acetone is adopted as media agent to effectively achieve homogenous dispersion of the nano-scale silica filler. The acetone also acts as diluents to reduce viscosity before the curing phase of epoxy resin and enables bubbles to escape from being trapped. Through partial discharge (PD) and surface aging tests, it is illustrated that the inception of surface discharge of the proposed NDM is relatively higher than that of the non-filled counterpart, and a better PD resistivity was observed in the negative half cycle regarding to applied AC voltage. Results of surface aging test indicate that surface discharge activity is retarded over the test conducting time. By contrast, surface discharge developed to the opposite way on the non-filled sample. Therefore, the proposed NDM could provide better safety reliability and lower maintenance cost to industrial application compared with nonfilled conventional epoxy resin.

Microscopic ion fluxes in plasma-aided nanofabrication of ordered carbon nanotip structures

Three-dimensional topography of microscopic ion fluxes in the reactive hydrocarbon-based plasma-aided nanofabrication of ordered arrays of vertically aligned single-crystalline carbon nanotip microemitter structures is simulated by using a Monte Carlo technique. The individual ion trajectories are computed by integrating the ion equations of motion in the electrostatic field created by a biased nanostructured substrate. It is shown that the ion flux focusing onto carbon nanotips is more efficient under the conditions of low potential drop Us across the near-substrate plasma sheath. Under low- Us conditions, the ion current density onto the surface of individual nanotips is higher for higher-aspect-ratio nanotips and can exceed the mean ion current density onto the entire nanopattern in up to approximately five times. This effect becomes less pronounced with increasing the substrate bias, with the mean relative enhancement of the ion current density ξi not exceeding ∼1.7. The value of ξi is higher in denser plasmas and behaves differently with the electron temperature Te depending on the substrate bias. When the substrate bias is low, ξi decreases with Te, with the opposite tendency under higher- Us conditions. The results are relevant to the plasma-enhanced chemical-vapor deposition of ordered large-area nanopatterns of vertically aligned carbon nanotips, nanofibers, and nanopyramidal microemitter structures for flat-panel display applications. © 2005 American Institute of Physics.

Templated i-PVD of metallic nanodot arrays

The results of numerical simulation of plasma-based, porous, template-assisted nanofabrication of Au nanodot arrays on highly-doped silicon taking into account typical electron density of low-temperature plasma of 1017-1018 m-3 and electron temperature of 2-5 eV are reported here. Three-dimensional microscopic topography of ion flux distribution over the outer and inner surfaces of the nanoporous template is obtained via numerical simulation of Au ion trajectories in the plasma sheath, in the close proximity of, and inside the nanopores. It is shown that, by manipulating the electron temperature, the cross-sheath potential drop, and by additionally altering the structure of the nanoporous template, one can control the ion fluxes within the nanopores, and eventually maximize the ion deposition onto the top surface of the developing crystalline Au nanodots (see top panel in the figure). In the same time, this procedure allows one to minimize amorphous deposits on the sidewalls that clutter and may eventually close the nanopores, thus disrupting the nanodot growth process, as it is shown in the bottom panel in the figure on the right.

Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders

The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.

Proactive safety assessment in roadwork zones : a synthesis of surrogate measures of safety

Work zone safety studies have traditionally relied on historical crash records—an approach which is reactive in nature as it requires crashes to accumulate first before taking any preventive actions. However, detailed and accurate data on work zone crashes are often not available, as is the case for Australian road work zones. The lack of reliable safety records and the reactive nature of the crash-based safety analysis approach motivated this research to seek alternative and proactive measures of safety. Various surrogate measures of safety have been developed in the traffic safety literature including time to collision, time to accident, gap time, post encroachment time, required deceleration rate, proportion of stopping distances, lateral distance to departure, and time to departure. These measures express how close road-user(s) are from a potential crash by analysing their movement trajectories. A review of this fast-growing literature is presented in this paper from the viewpoint of applying the measures to untangle work zone safety issues. The review revealed that the use of the surrogate measures is very limited for analysing work zone safety, although numerous studies have used these measures for analysing safety in other parts of the road network, such as intersections and motorway ramps. There exist great opportunities for adopting this proactive safety assessment approach to transform work zone safety for both roadworkers and motorists.

Rough Seas

Favel Parrett’s second novel, When the Night Comes, opens with its teenage protagonist Isla lying awake in her bunk on a night ferry to Tasmania in the mid-1980s, ‘waiting for the rough seas’. Her younger brother sleeps beside her, and her distracted, emotionally distant mother – the kind of woman who is ‘always sitting places by herself in the night’ – is smoking on deck. Together, the three are weathering the roiling overnight passage in order to escape a violent past and make a new life in Hobart. The rough seas the novel goes on to navigate are, as one might expect, both literal and metaphorical...

Helsinki adventure : inside the ‘design nation’

A travel article about Helsinki exploring the city's design culture. I’M often told that I’m from Finland. Even those who’ve known me for years confuse it with my birthplace, which is, in fact, Iceland. I’m not sure why the two countries are mixed up in this way, but it might be that Iceland and Finland are, in a sense, the “other” Scandinavian nations – on different sides of the Nordic world, but in the mind joined as its outer borders...