Beyond simple imaging with energetic beams – nanopatterning, correlative microscopy and statistical analysis of inclusions

Electron microscopy (EM) has advanced in an exponential way since the first transmission electron microscope (TEM) was built in the 1930’s. The urge to ‘see’ things is an essential part of human nature (talk of ‘seeing is believing’) and apart from scanning tunnel microscopes which give information about the surface, EM is the only imaging technology capable of really visualising atomic structures in depth down to single atoms. With the development of nanotechnology the demand to image and analyse small things has become even greater and electron microscopes have found their way from highly delicate and sophisticated research grade instruments to key-turn and even bench-top instruments for everyday use in every materials research lab on the planet. The semiconductor industry is as dependent on the use of EM as life sciences and pharmaceutical industry. With this generalisation of use for imaging, the need to deploy advanced uses of EM has become more and more apparent. The combination of several coinciding beams (electron, ion and even light) to create DualBeam or TripleBeam instruments for instance enhances the usefulness from pure imaging to manipulating on the nanoscale. And when it comes to the analytic power of EM with the many ways the highly energetic electrons and ions interact with the matter in the specimen there is a plethora of niches which evolved during the last two decades, specialising in every kind of analysis that can be thought of and combined with EM. In the course of this study the emphasis was placed on the application of these advanced analytical EM techniques in the context of multiscale and multimodal microscopy – multiscale meaning across length scales from micrometres or larger to nanometres, multimodal meaning numerous techniques applied to the same sample volume in a correlative manner. In order to demonstrate the breadth and potential of the multiscale and multimodal concept an integration of it was attempted in two areas: I) Biocompatible materials using polycrystalline stainless steel and II) Semiconductors using thin multiferroic films. I) The motivation to use stainless steel (316L medical grade) comes from the potential modulation of endothelial cell growth which can have a big impact on the improvement of cardio-vascular stents – which are mainly made of 316L – through nano-texturing of the stent surface by focused ion beam (FIB) lithography. Patterning with FIB has never been reported before in connection with stents and cell growth and in order to gain a better understanding of the beam-substrate interaction during patterning a correlative microscopy approach was used to illuminate the patterning process from many possible angles. Electron backscattering diffraction (EBSD) was used to analyse the crystallographic structure, FIB was used for the patterning and simultaneously visualising the crystal structure as part of the monitoring process, scanning electron microscopy (SEM) and atomic force microscopy (AFM) were employed to analyse the topography and the final step being 3D visualisation through serial FIB/SEM sectioning. II) The motivation for the use of thin multiferroic films stems from the ever-growing demand for increased data storage at lesser and lesser energy consumption. The Aurivillius phase material used in this study has a high potential in this area. Yet it is necessary to show clearly that the film is really multiferroic and no second phase inclusions are present even at very low concentrations – ~0.1vol% could already be problematic. Thus, in this study a technique was developed to analyse ultra-low density inclusions in thin multiferroic films down to concentrations of 0.01%. The goal achieved was a complete structural and compositional analysis of the films which required identification of second phase inclusions (through elemental analysis EDX(Energy Dispersive X-ray)), localise them (employing 72 hour EDX mapping in the SEM), isolate them for the TEM (using FIB) and give an upper confidence limit of 99.5% to the influence of the inclusions on the magnetic behaviour of the main phase (statistical analysis).

Characterization and analysis of the exogenous application of selected phytohormones on C. reinhardtii metabolism

Gemstone Team Genes to Fuels

WormSizer: high-throughput analysis of nematode size and shape.

The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.

Transcriptome analysis of sulfate deficiency response in marine microalga Emiliania huxleyi

Summary The response to sulfate deficiency of plants and freshwater green algae has been extensively analysed by system biology approaches. By contrast, seawater sulfate concentration is high and very little is known about the sulfur metabolism of marine organisms. Here, we used a combination of metabolite analysis and transcriptomics to analyse the response of the marine microalga Emiliania huxleyi as it acclimated to sulfate limitation. Lowering sulfate availability in artificial seawater from 25 to 5 mM resulted in significant reduction in growth and intracellular concentrations of dimethylsulfoniopropionate and glutathione. Sulfate-limited E. huxleyi cells showed increased sulfate uptake but sulfate reduction to sulfite did not seem to be regulated. Sulfate limitation in E. huxleyi affected expression of 1718 genes. The vast majority of these genes were upregulated, including genes involved in carbohydrate and lipid metabolism, and genes involved in the general stress response. The acclimation response of E. huxleyi to sulfate deficiency shows several similarities to the well-described responses of Arabidopsis and Chlamydomonas, but also has many unique features. This dataset shows that even though E. huxleyi is adapted to constitutively high sulfate concentration, it retains the ability to re-program its gene expression in response to reduced sulfate availability.

Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel

Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S-trnI-trnA-23S-5S, rbcL-rbcS and rpl12-rps31-rpl9 regions and the mitochondrial cox2–3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128 000 bp and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20 000 bp) in the Hurd Deep, an enigmatic trench in the English Channel.

Cultural policy models and cultural facilities models: from national to local models. Analysis of Barcelona’s case

The development of cultural policy analysis by social science has been produced a theorization about cultural policy models from sociology and political science. This analysis shows the influence of the national model of cultural policy on the forms of governance and management of cultural facilities. However, in this paper we will defend that currently the local model of cultural policy decisively influences the model of cultural institutions. This is explained by the growing importance of culture in local development strategies. In order to demonstrate this we will analyze the case of the Barcelona Model of local development and cultural policy, that is characterized for the level of local government leadership, multilevel governance, the use of culture in urban planning processes and a tendency to use public-private partnership in public management. This Model influences the genesis and development of the cultural facilities and it produces a singular and relatively successful model.

From the transformation to the bancarization of the spanishsaving banks: an analysis of the results pursued

This research arises due to the current restructuring process in which is immersed the Spanish banking sector. The above mentioned process is carried out to try to reduce the doubts on the viability of the bank companies to average and long term and to be able to return again the confidence in the sector. Though the economic and financial crisis has concerned the whole banking sector, the subsector of the Spanish savings banks is the one that has experienced a major number of integrations (articulated by means of mergers, absorptions and across Institutional Protection Schemes -IPSs-), and the one that has met submitted to the bancarization process. Considering what has been said, the present paper analyses Spanish saving banks to try to discern whether thanks to that process the objectives pursued by the bank rearrangement have been fulfilled. To do this, the evolution of some important financial variables will be studied over a long period of time (1999-2012). The results suggest that not all the savings banks have seen improved their ratios of efficiency, solvency, financial gap and social work, which indicates that there is still much to be done in order to rectify the problems affecting the studied sector.

Determining factors of the innovative behavior of cooperatives: an analysis of the case of Castilla y León

Cooperatives have a long historical experience in the Spanish economy and have demonstrated their ability to compete against traditional firms in the market. To maintain this capability, while taking advantage of the competitive advantages associated with their idiosyncrasies as social economy enterprises, they should take into consideration that the economy is increasingly globalized and increasingly knowledge-based, especially with regards to technological content. As a consequence, the innovative capacity appears to be a key aspect in order to be able to challenge competitors. This article characterizes the innovative behavior of cooperatives in the region of Castile and Leon and analyses the internal and external factors affecting their innovative performance, based on data from a survey of 581 cooperatives. The results of the empirical analysis, which is performed by multivariate binary logistic regression on various types of innovation, lead us to identify the size of the organizations, the existence of planning, the R & D activities and the human capital as the main determining factors.

Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495

Aminobacter lissarensis CC495 is an aerobic facultative methylotroph capable of growth on glucose, glycerol, pyruvate and methylamine as well as the methyl halides methyl chloride and methyl bromide. Previously, cells grown on methyl chloride have been shown to express two polypeptides with apparent molecular masses of 67 and 29 kDa. The 67 kDa protein was purified and identified as a halomethane:bisulfide/halide ion methyltransferase. This study describes a single gene cluster in A. lissarensis CC495 containing the methyl halide utilisation genes cmuB, cmuA, cmuC, orf 188, paaE and hutI The genes correspond to the same order and have a high similarity to a gene cluster found in Aminobacter ciceronei IMB-1 and Hyphomicrobium chloromethanicum strain CM2 indicating that genes encoding methyl halide degradation are highly conserved in these strains. (c) 2005 Federation of European Microbiological Societies. Published by Elsevier, B.V. All rights reserved.

Solid-state analysis of low-melting 1,3-dialkylimidazolium hexafluorophosphate salts (ionic liquids) by combined x-ray crystallographic and computational analyses

The interactions of ions in the solid state for a series of representative 1,3-dialkylimidazolium hexafluorophosphate salts (either ionic liquids or closely related) have been examined by crystallographic analysis, combined with the theoretical estimation of crystal-packing densities and lattice-interaction energies. Efficient close-packing of the ions in the crystalline states is observed, but there was no compelling evidence for specific directional hydrogen-bonding to the hexafluorophosphate anions or the formation of interstitial voids. The close-packing efficiency is supported by the theoretical calculation of ion volumes, crystal lattice energies, and packing densities, which correlated well with experimental data. The crystal density of the salts can be predicted accurately from the summation of free ion volumes and lattice energies calculated. Of even more importance for future work, on these and related salts, the solid-state density of 1,3-dialkylimidazolium hexafluorophosphate salts can be predicted with reasonable accuracy purely on the basis of on ab initio free ion volumes, and this allows prediction of lattice energies without necessarily requiring the crystal structures.

A meta-analysis of latitudinal variations in life-history traits of roach, Rutilus rutilus, over its geographical range: linear or non-linear relationships?

1. We collated information from the literature on life history traits of the roach (a generalist freshwater fish), and analysed variation in absolute fecundity, von Bertalanffy parameters, and reproductive lifespan in relation to latitude, using both linear and non-linear regression models. We hypothesized that because most life history traits are dependent on growth rate, and growth rate is non-linearly related with temperature, it was likely that when analysed over the whole distribution range of roach, variation in key life history traits would show non-linear patterns with latitude.

Analysis of information leakage from encrypted Skype conversations

Voice over IP (VoIP) has experienced a tremendous growth over the last few years and is now widely used among the population and for business purposes. The security of such VoIP systems is often assumed, creating a false sense of privacy. This paper investigates in detail the leakage of information from Skype, a widely used and protected VoIP application. Experiments have shown that isolated phonemes can be classified and given sentences identified. By using the dynamic time warping (DTW) algorithm, frequently used in speech processing, an accuracy of 60% can be reached. The results can be further improved by choosing specific training data and reach an accuracy of 83% under specific conditions. The initial results being speaker dependent, an approach involving the Kalman filter is proposed to extract the kernel of all training signals.

After the Party the Hangover?: An Analysis of ‘Post-Celtic Tiger’ Ireland in the Light of the February 2011 elections’

The election of February 2011 was dominated by the International Monetary Fund/European Central Bank bailout of November 2010, the state of the public finances, the ongoing Irish banking crisis, and the disastrous state of the economy with rising unemployment, emigration and collapsing international competiveness. After years of phenomenal economic growth (at least as measured by orthodox economic measurements such as gross domestic product (GDP) and foreign direct investment), known as the 'Celtic Tiger‘, during which a bloated construction industry accounted for a quarter of GDP and Irish banks sank nearly a third of their lending in construction projects, Ireland has entered a 'post-Celtic Tiger‘ era. This article offers a critical analysis outlining some political, economic and cultural issues of this election as heralding a decisive stage in the 'post-Celtic Tiger' development of the Republic of Ireland, and suggests that what is required at this present historical moment is that a different development model be articulated by the Irish state and wider society.

Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation

The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in knockout mice and de-regulation of TP63 expression in neoplasia altering the tumour suppressive roles of the TP53 family. In order to define the normal role played by TP63 and provide the basis for better understanding how this network is perturbed in disease, we used chromatin immunoprecipitation combined with massively parallel sequencing (ChIP-seq) to identify >7500 high-confidence TP63-binding regions across the entire genome, in primary human neonatal foreskin keratinocytes (HFKs). Using integrative strategies, we demonstrate that only a subset of these sites are bound by TP53 in response to DNA damage. We identify a role for TP63 in transcriptional regulation of multiple genes genetically linked to cleft palate and identify AP-2alpha (TFAP2A) as a co-regulator of a subset of these genes. We further demonstrate that AP-2gamma (TFAP2C) can bind a subset of these regions and that acute depletion of either TFAP2A or TFAP2C alone is sufficient to reduce terminal differentiation of organotypic epidermal skin equivalents, indicating overlapping physiological functions with TP63.

Numerical analysis of stiffener runout sections

The recent trend of incorporating more composite material in primary aircraft structures has highlighted the vulnerability of stiffened aerostructures to through-thickness stresses, which may lead to delamination and debonding at the skin-stiffener interface, leading to collapse. Stiffener runout regions are particularly susceptible to this problem and cannot be avoided due to the necessity to terminate stiffeners at rib intersections or at cutouts, interrupting the stiffener load path. In this paper, experimental tests relating to two different stiffener runout specimens are presented and the failure modes of both specimens are discussed in detail. A thinner-skinned specimen showed sudden and unstable crack propagation, while a thicker-skinned specimen showed initially unstable but subsequent stable crack growth. Detailed finite element models of the two specimens are developed, and it is shown how such models can explain and predict the behaviour and failure mode of stiffener runouts. The models contain continuum shell elements to model the skin and stiffener, while cohesive elements using a traction-separation law are placed at the skin-stiffener interface to effectively model the debonding which promotes structural failure.