Quantification of ruminal Clostridium proteoclasticum by real-time PCR using a molecular beacon approach

Aims: All members of the ruminal Butyrivibrio group convert linoleic acid (cis-9,cis-12-18 : 2) via conjugated 18 : 2 metabolites (mainly cis-9,trans-11-18 : 2, conjugated linoleic acid) to vaccenic acid (trans-11-18 : 1), but only members of a small branch, which includes Clostridium proteoclasticum, of this heterogeneous group further reduce vaccenic acid to stearic acid (18 : 0, SA). The aims of this study were to develop a real-time polymerase chain reaction (PCR) assay that would detect and quantify these key SA producers and to use this method to detect diet-associated changes in their populations in ruminal digesta of lactating cows. Materials and Results: The use of primers targeting the 16S rRNA gene of Cl. proteoclasticum was not sufficiently specific when only binding dyes were used for detection in real-time PCR. Their sequences were too similar to some nonproducing strains. A molecular beacon probe was designed specifically to detect and quantify the 16S rRNA genes of the Cl. proteoclasticum subgroup. The probe was characterized by its melting curve and validated using five SA-producing and ten nonproducing Butyrivibrio-like strains and 13 other common ruminal bacteria. Analysis of ruminal digesta collected from dairy cows fed different proportions of starch and fibre indicated a Cl. proteoclasticum population of 2-9% of the eubacterial community. The influence of diet on numbers of these bacteria was less than variations between individual cows. Conclusion: A molecular beacon approach in qPCR enables the detection of Cl. proteoclasticum in ruminal digesta. Their numbers are highly variable between individual animals. Signifance and Impact of the Study: SA producers are fundamental to the flow of polyunsaturated fatty acid and vaccenic acid from the rumen. The method described here enabled preliminary information to be obtained about the size of this population. Further application of the method to digesta samples from cows fed diets of more variable composition should enable us to understand how to control these bacteria in order to enhance the nutritional characteristics of ruminant-derived foods, including milk and beef.

Use of global gene expression patterns in mechanistic studies of oestrogen action in MCF7 human breast cancer cells

Over the years, the MCF7 human breast cancer cell line has provided a model system for the study of cellular and molecular mechanisms in oestrogen regulation of cell proliferation and in progression to oestrogen and antioestrogen independent growth. Global gene expression profiling has shown that oestrogen action in MCF7 cells involves the coordinated regulation of hundreds of genes across a wide range of functional groupings and that more genes are down regulated than upregulated. Adaptation to long-term oestrogen deprivation, which results in loss of oestrogen-responsive growth, involves alterations to gene patterns not only at early time points (0-4 weeks) but continuing through to later times (20-55 weeks), and even involves alterations to patterns of oestrogen-regulated gene expression. Only 48% of the genes which were regulated >= 2-fold by oestradiol in oestrogen-responsive cells retained this responsiveness after long-term oestrogen deprivation but other genes developed de novo oestrogen regulation. Long-term exposure to fulvestrant, which resulted in loss of growth inhibition by the antioestrogen, resulted in some very large fold changes in gene expression up to 10,000-fold. Comparison of gene profiles produced by environmental chemicals with oestrogenic properties showed that each ligand gave its own unique expression profile which suggests that environmental oestrogens entering the human breast may give rise to a more complex web of interference in cell function than simply mimicking oestrogen action at inappropriate times. (C) 2009 Elsevier Ltd. All rights reserved.

The potential for the use of agent-based models in ecotoxicology

This chapter introduces ABMs, their construction, and the pros and cons of their use. Although relatively new, agent-basedmodels (ABMs) have great potential for use in ecotoxicological research – their primary advantage being the realistic simulations that can be constructed and particularly their explicit handling of space and time in simulations. Examples are provided of their use in ecotoxicology primarily exemplified by different implementations of the ALMaSS system. These examples presented demonstrate how multiple stressors, landscape structure, details regarding toxicology, animal behavior, and socioeconomic effects can and should be taken into account when constructing simulations for risk assessment. Like ecological systems, in ABMs the behavior at the system level is not simply the mean of the component responses, but the sum of the often nonlinear interactions between components in the system; hence this modeling approach opens the door to implementing and testing much more realistic and holistic ecotoxicological models than are currently used.

The use of bioluminescence for monitoring in planta growth dynamics of a Pseudomonas syringae plant pathogen

The use of bioluminescence was evaluated as a tool to study Pseudomonas syringae population dynamics in susceptible and resistant plant environments. Plasmid pGLITE, containing the luxCDABE genes from Photorhabdus luminescens, was introduced into Pseudomonas syringae pv. phaseolicola race 7 strain 1449B, a Gram-negative pathogen of bean (Phaseolus vulgaris). Bacteria recovered from plant tissue over a five-day period were enumerated by counting numbers of colony forming units and by measurement of bioluminescence. Direct measurement of bioluminescence from leaf disc homogenates consistently reflected bacterial growth as determined by viable counting, but also detected subtle effects of the plant resistance response on bacterial viability. This bioluminescence procedure enables real time measurement of bacterial metabolism and population dynamics in planta, obviates the need to carry out labour intensive and time consuming traditional enumeration techniques and provides a sensitive assay for studying plant effects on bacterial cells.

Reaching for the skies: Time and turbulence in digital technologies and practices

This research examines dynamics associated with new representational technologies in complex organizations through a study of the use of a Single Model Environment, prototyping and simulation tools in the mega-project to construct Terminal 5 at Heathrow Airport, London. The ambition of the client, BAA. was to change industrial practices reducing project costs and time to delivery through new contractual arrangements and new digitally-enabled collaborative ways of working. The research highlights changes over time and addresses two areas of 'turbulence' in the use of: 1) technologies, where there is a dynamic tension between desires to constantly improve, change and update digital technologies and the need to standardise practices, maintaining and defending the overall integrity of the system; and 2) representations, where dynamics result from the responsibilities and liabilities associated with sharing of digital representations and a lack of trust in the validity of data from other firms. These dynamics are tracked across three stages of this well-managed and innovative project and indicate the generic need to treat digital infrastructure as an ongoing strategic issue.

Preliminary results from a real time control system using optical information

Successful results from training an adaptive controller to use optical information to balance an inverted pendulum are presented in comparison to the training requirements using traditional controller inputs. Results from research into the psychology of the sense of balance in humans are presented as the motivation for the investigation of this new type of controller. The simulated model of the inverted pendulum and the virtual reality environments used to provide the optical input are described The successful introduction of optical information is found to require the preservation of at least two of the traditional input types and entail increased training time for the adaptive controller and reduced performance (measured as the time the pendulum remains upright).

Empirical mode decomposition: a novel technique for the study of tremor time series

Tremor is a clinical feature characterized by oscillations of a part of the body. The detection and study of tremor is an important step in investigations seeking to explain underlying control strategies of the central nervous system under natural (or physiological) and pathological conditions. It is well established that tremorous activity is composed of deterministic and stochastic components. For this reason, the use of digital signal processing techniques (DSP) which take into account the nonlinearity and nonstationarity of such signals may bring new information into the signal analysis which is often obscured by traditional linear techniques (e.g. Fourier analysis). In this context, this paper introduces the application of the empirical mode decomposition (EMD) and Hilbert spectrum (HS), which are relatively new DSP techniques for the analysis of nonlinear and nonstationary time-series, for the study of tremor. Our results, obtained from the analysis of experimental signals collected from 31 patients with different neurological conditions, showed that the EMD could automatically decompose acquired signals into basic components, called intrinsic mode functions (IMFs), representing tremorous and voluntary activity. The identification of a physical meaning for IMFs in the context of tremor analysis suggests an alternative and new way of detecting tremorous activity. These results may be relevant for those applications requiring automatic detection of tremor. Furthermore, the energy of IMFs was visualized as a function of time and frequency by means of the HS. This analysis showed that the variation of energy of tremorous and voluntary activity could be distinguished and characterized on the HS. Such results may be relevant for those applications aiming to identify neurological disorders. In general, both the HS and EMD demonstrated to be very useful to perform objective analysis of any kind of tremor and can therefore be potentially used to perform functional assessment.

Orthogonal space-time block codes for free-space IM/DD optical links

Use of orthogonal space-time block codes (STBCs) with multiple transmitters and receivers can improve signal quality. However, in optical intensity modulated signals, output of the transmitter is non-negative and hence standard orthogonal STBC schemes need to be modified. A generalised framework for applying orthogonal STBCs for free-space IM/DD optical links is presented.

Proposing a way forward: a review of standardisation in the use of age categories and ageing techniques in osteological analysis (2004 to 2009)

This study assesses the current state of adult skeletal age-at-death estimation in biological anthropology through analysis of data published in recent research articles from three major anthropological and archaeological journals (2004–2009). The most commonly used adult ageing methods, age of ‘adulthood’, age ranges and the maximum age reported for ‘mature’ adults were compared. The results showed a wide range of variability in the age at which individuals were determined to be adult (from 14 to 25 years), uneven age ranges, a lack of standardisation in the use of descriptive age categories and the inappropriate application of some ageing methods for the sample being examined. Such discrepancies make comparisons between skeletal samples difficult, while the inappropriate use of some techniques make the resultant age estimations unreliable. At a time when national and even global comparisons of past health are becoming prominent, standardisation in the terminology and age categories used to define adults within each sample is fundamental. It is hoped that this research will prompt discussions in the osteological community (both nationally and internationally) about what defines an ‘adult’, how to standardise the age ranges that we use and how individuals should be assigned to each age category. Skeletal markers have been proposed to help physically identify ‘adult’ individuals.

Efficient on the fly calculation of time correlation functions in computer simulations

Time correlation functions yield profound information about the dynamics of a physical system and hence are frequently calculated in computer simulations. For systems whose dynamics span a wide range of time, currently used methods require significant computer time and memory. In this paper, we discuss the multiple-tau correlator method for the efficient calculation of accurate time correlation functions on the fly during computer simulations. The multiple-tau correlator is efficacious in terms of computational requirements and can be tuned to the desired level of accuracy. Further, we derive estimates for the error arising from the use of the multiple-tau correlator and extend it for use in the calculation of mean-square particle displacements and dynamic structure factors. The method described here, in hardware implementation, is routinely used in light scattering experiments but has not yet found widespread use in computer simulations.

Time-dependent orientation coupling in equilibrium polymer melts

The motion in concentrated polymer systems is described by either the Rouse or the reptation model, which both assume that the relaxation of each polymer chain is independent of the surrounding chains. This, however, is in contradiction with several experiments. In this Letter, we propose a universal description of orientation coupling in polymer melts in terms of the time-dependent coupling parameter κ(t). We use molecular dynamics simulations to show that the coupling parameter increases with time, reaching about 50% at long times, independently of the chain length or blend composition. This leads to predictions of component dynamics in mixtures of different molecular weights from the knowledge of monodisperse dynamics for unentangled melts. Finally, we demonstrate that entanglements do not play a significant role in the observed coupling. © 2010 The American Physical Society

An Exponentially Convergent Nonpolynomial Finite Element Method for Time-Harmonic Scattering from Polygons

In recent years nonpolynomial finite element methods have received increasing attention for the efficient solution of wave problems. As with their close cousin the method of particular solutions, high efficiency comes from using solutions to the Helmholtz equation as basis functions. We present and analyze such a method for the scattering of two-dimensional scalar waves from a polygonal domain that achieves exponential convergence purely by increasing the number of basis functions in each element. Key ingredients are the use of basis functions that capture the singularities at corners and the representation of the scattered field towards infinity by a combination of fundamental solutions. The solution is obtained by minimizing a least-squares functional, which we discretize in such a way that a matrix least-squares problem is obtained. We give computable exponential bounds on the rate of convergence of the least-squares functional that are in very good agreement with the observed numerical convergence. Challenging numerical examples, including a nonconvex polygon with several corner singularities, and a cavity domain, are solved to around 10 digits of accuracy with a few seconds of CPU time. The examples are implemented concisely with MPSpack, a MATLAB toolbox for wave computations with nonpolynomial basis functions, developed by the authors. A code example is included.

Taking time to understand: articulating relationships between technologies and organizations

Dynamic relationships between technologies and organizations are investigated through research on digital visualization technologies and their use in the construction sector. Theoretical work highlights mutual adaptation between technologies and organizations but does not explain instances of sustained, sudden, or increasing maladaptation. By focusing on the technological field, I draw attention to hierarchical structuring around inter-dependent levels of technology; technological priorities of diverse groups; power asymmetries and disjunctures between contexts of development and use. For complex technologies, such as digital technologies, I argue these field-level features explain why organizations peripheral to the field may experience difficulty using emerging technology.

Time-resolved gas-phase kinetic, quantum chemical and RRKM studies of reactions of silylene with cyclic ethers

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with oxirane, oxetane, and tetrahydrofuran (THF). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at four or five temperatures in the range 294-605 K. All three reactions showed pressure dependences characteristic of third-body-assisted association reactions with, surprisingly, SiH2 + oxirane showing the least and SiH2 + THF showing the most pressure dependence. The second-order rate constants obtained by extrapolation to the high-pressure limits at each temperature fitted the Arrhenius equations where the error limits are single standard deviations: log(k(oxirane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.03 +/- 0.07) + (5.70 +/- 0.51) kJ mol(-1)/RT In 10 log(k(oxetane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.17 +/- 0.11) + (9.04 +/- 0.78) kJ mol(-1)/RT In 10 log(k(THF)(infinity)/cm(3) molecule(-1) s(-1)) = (-10.59 +/- 0.10) + (5.76 +/- 0.65) kJ mol(-1)/RT In 10 Binding-energy values of 77, 97, and 92 kJ mol(-1) have been obtained for the donor-acceptor complexes of SiH2 with oxirane, oxetane, and THF, respectively, by means of quantum chemical (ab initio) calculations carried Out at the G3 level. The use of these values to model the pressure dependences of these reactions, via RRKM theory, provided a good fit only in the case of SiH2 + THF. The lack of fit in the other two cases is attributed to further reaction pathways for the association complexes of SiH2 with oxirane and oxetane. The finding of ethene as a product of the SiH2 + oxirane reaction supports a pathway leading to H2Si=O + C2H4 predicted by the theoretical calculations of Apeloig and Sklenak.

The use of trajectory cluster analysis to interpret trace gas measurements at Mace Head, Ireland

A first step in interpreting the wide variation in trace gas concentrations measured over time at a given site is to classify the data according to the prevailing weather conditions. In order to classify measurements made during two intensive field campaigns at Mace Head, on the west coast of Ireland, an objective method of assigning data to different weather types has been developed. Air-mass back trajectories calculated using winds from ECMWF analyses, arriving at the site in 1995–1997, were allocated to clusters based on a statistical analysis of the latitude, longitude and pressure of the trajectory at 12 h intervals over 5 days. The robustness of the analysis was assessed by using an ensemble of back trajectories calculated for four points around Mace Head. Separate analyses were made for each of the 3 years, and for four 3-month periods. The use of these clusters in classifying ground-based ozone measurements at Mace Head is described, including the need to exclude data which have been influenced by local perturbations to the regional flow pattern, for example, by sea breezes. Even with a limited data set, based on 2 months of intensive field measurements in 1996 and 1997, there are statistically significant differences in ozone concentrations in air from the different clusters. The limitations of this type of analysis for classification and interpretation of ground-based chemistry measurements are discussed.